索引

Bonferroni 補正.................................................................................................... 272
boolean indexing................................................................................................ 167
Box-Cox 変換........................................................................................................ 299
boxplot()................................................................................................................. 235
Brunner-Munzel 検定..................................................................................... 262
記号・数字!..........................................................................................................................................28#..........................................................................................................................................40C%..........................................................................................................................................26

cDNA ライブラリ.............................................................................................. 286%%.......................................................................................................................................27clustermap()................................................................................... 249, 344, 347/....................................................................................................................................... 149

concat()......................................................................................................... 189, 293//.................................................................................................................................... 149

concatenate()...................................................................................................... 389?..........................................................................................................................................26CSV............................................................................................................................... 287__len__()................................................................................................................. 112

cumsum().................................................................................................................... 158__repr__().............................................................................................................. 11210x Genomics............................................................................................. 286, 389
DDataFrame................................................................................................... 147, 153
A

DBSCAN.................................................................................................................. 369

add_subplot()...................................................................................................... 252

DDBJ........................................................................................................................... 124

AIC.................................................................................................................... 278, 358

def.....................................................................................................................................74

Anaconda....................................................................................................................15

DESeq2........................................................................................................... 276, 279

anndata...................................................................................................................... 388

dir()............................................................................................................................ 104

annotate().............................................................................................................. 315

dispersion parameter...................................................................................... 279

append().......................................................................................................................53

doublet....................................................................................................................... 294

apply()....................................................................................................................... 182

drop_duplicates()............................................................................................ 177

argsort()................................................................................................................. 387
array()....................................................................................................................... 374
astype().................................................................................................................... 377

Eat.................................................................................................................................... 162

edgeR.......................................................................................................................... 276Automagic..................................................................................................................26

Elbow method...................................................................................................... 357

Axes クラス............................................................................................................ 226

EMBL.......................................................................................................................... 124

axis............................................................................................................................... 381
FB

FAI ファイル......................................................................................................... 122bar()............................................................................................................................ 244

familywise error rate...................................................................................... 272

BCBioGFF............................................................................................................... 141

FASTA 形式.......................................................................................................... 105

Benjamini-Hochberg 法................................................................................ 273

fastcluster................................................................................................................ 346

BIC................................................................................................................................ 358

FDR.............................................................................................................................. 273

Biopython...................................................................................................... 114, 201

Figure クラス........................................................................................................ 226

Bokeh.......................................................................................................................... 223

fillna().................................................................................................................... 175399

fit_predict()...................................................................................................... 353

iteritems()............................................................................................................ 186

float64.......................................................................................................................... 148

iterrows().............................................................................................................. 186

fold change............................................................................................................. 239

IVIS.............................................................................................................................. 339

for 文.........................................................................................................68, 185, 292
FPKM.............................................................................................................. 211, 265
FPM............................................................................................................................. 209J

f 文字列....................................................................................................................... 110Jaccard 距離........................................................................................................... 344
JBrowse..................................................................................................................... 138
join()......................................................................................................................... 191

Gjointplot()............................................................................................................ 240

GC 含量...................................................................................................................... 106

JoyPy........................................................................................................................... 234

GenBank 形式........................................................................................................ 124

Jupyter Notebook.................................................................................................19GFF................................................................................................................... 138, 201

JupyterLab................................................................................................................32

gffread........................................................................................................................ 139
GFF ファイル...........................................................................................................84
GitHub...........................................................................................................................20K

GMOD........................................................................................................................ 138

k -means クラスタリング............................................................................. 352

Google Colaboratory...........................................................................................33

KEGG.......................................................................................................................... 114

GPU.................................................................................................................................33

Kruskal-Wallis 検定......................................................................................... 262

GridSpec().............................................................................................................. 254

k 近傍グラフ................................................................................................ 330, 358

groupby()................................................................................................................. 196
GTF.............................................................................................................................. 139
Llambda 式.....................................................................................................................57H

LaTeX...........................................................................................................................23

HDBSCAN.............................................................................................................. 369

leftjoin......................................................................................................................... 193

head()......................................................................................................................... 204

Leiden 法........................................................................................................ 361, 398

Hi-C 解析.................................................................................................................. 304

len()...............................................................................................................................51

hist()......................................................................................................................... 231

lenged().................................................................................................................... 243
linspace().............................................................................................................. 376
loadtxt()................................................................................................................. 290

I

loc................................................................................................................................. 163

iat................................................................................................................................. 163
id()..................................................................................................................................67

400

IDE...................................................................................................................................33

M

if 文...................................................................................................................................68

macOS...........................................................................................................................15

IGV................................................................................................................................ 141

Maker......................................................................................................................... 138

import............................................................................................................................77

Mann-Whitney の U 検定............................................................................. 262

innerjoin................................................................................................................. 193

map 関数................................................................................................................... 181

INSDC........................................................................................................................ 124

MATLAB................................................................................................................ 228

int64.............................................................................................................................. 148

Matplotlib.........................................................................................................29, 223

interpolate()...................................................................................................... 176

matplotlib_venn................................................................................................. 251

独習Python バイオ情報解析

matrix balancing................................................................................................ 304

plot()......................................................................................................................... 242

MA プロット.......................................................................................................... 238

Plotly........................................................................................................................... 223

MDS............................................................................................................................. 319

print()..........................................................................................................................41

mean()......................................................................................................................... 158

pyenv.............................................................................................................................16

merge()....................................................................................................................... 192

pyfaidx モジュール........................................................................................... 122

MM............................................................................................................................... 289

Python...........................................................................................................................14mmread().................................................................................................................... 290

Python3........................................................................................................................16mRNA......................................................................................................................... 139

Python のバージョン..........................................................................................16

multi FASTA....................................................................................................... 108

p 値................................................................................................................................ 261

MultiIndex................................................................................................... 194, 303
multiplet.................................................................................................................... 294
Qq 値................................................................................................................................ 273
NN50................................................................................................................................ 119
NCBI............................................................................................................................ 114

RNMDS......................................................................................................................... 319

range()..........................................................................................................................71

Notebook Extensions.........................................................................................30

Raw NBConvert セル.........................................................................................22NP 困難...................................................................................................................... 359

read_csv().............................................................................................................. 287

NumPy................................................................................................. 216, 374, 390

read_pickle()...................................................................................................... 306
readline().................................................................................................................85
RefSeq........................................................................................................................ 124

O

remove().......................................................................................................................53

object........................................................................................................................... 149

reshape()................................................................................................................. 378

object-oriented インターフェース........................................................ 227

return 文............................................................................................................75, 109

ones()......................................................................................................................... 376

RNA-Seq............................................................................................ 199, 225, 256open()............................................................................................................................82

RPKM.............................................................................................................. 211, 265
RPM............................................................................................................................. 209

Ppairplot().............................................................................................................. 241

S

pandas................................................................................................................29, 147

SAM................................................................................................................................93

PARC.......................................................................................................................... 368

SAUCIE.................................................................................................................... 369

partition()............................................................................................................ 362

savefig()................................................................................................................. 229

PCA.............................................................................................................................. 306

Scanpy............................................................................................................. 285, 388

PCoA........................................................................................................................... 319

scatter()...................................................................................................... 237, 308

PDB.............................................................................................................................. 114

scikit-learn........................................................................................ 308, 325, 353

pdist()....................................................................................................................... 362

scRNA-Seq............................................................................................................. 284

Pearson 相関係数..................................................................................... 267, 311

Seaborn...................................................................................................................... 223

PHATE...................................................................................................................... 339

self............................................................................................................................... 106

pickle................................................................................................................ 303, 306

SeqIO.......................................................................................................................... 114

pivot_table()...................................................................................................... 197

Series........................................................................................................................... 148

401

Seurat......................................................................................................................... 285

venn3()....................................................................................................................... 251

show()......................................................................................................................... 227

violinplot()......................................................................................................... 236

silhouette_samples()................................................................................... 357

VMR............................................................................................................................. 300

SNE............................................................................................................................... 320
sort_index()......................................................................................................... 158
sort_values()...................................................................................................... 159

W

sorted().......................................................................................................................54

while 文.........................................................................................................................68

source feature...................................................................................................... 129

with 構文......................................................................................................................82

Spearman 相関係数........................................................................................... 267

WSL2..............................................................................................................................15squareform()......................................................................................................... 362
SRA データベース............................................................................................. 200
state-based インターフェース................................................................. 228

Ystaticmethod.......................................................................................................... 112

yield 文........................................................................................................................ 109sum()............................................................................................................................ 157
ZTzeros()....................................................................................................................... 376

t-SNE............................................................................................................... 307, 317

Z スコア..................................................................................................................... 185

TATA ボックス.....................................................................................................97
to_csv()......................................................................................................... 197, 303
to_pickle()............................................................................................................ 303

あtoarray()................................................................................................................. 290

赤池情報量規準.................................................................................................... 358

TPM.................................................................................................................. 214, 265

アクセッション番号......................................................................................... 204

TPU.................................................................................................................................33

値.......................................................................................................................................63

train_test_split()......................................................................................... 337

アトリビュート.................................................................................................... 375

trajectory inference......................................................................................... 398

アノテーション......................................................................................... 124, 396

transpose()............................................................................................................ 381
try 〜 except 構文............................................................................................... 136
Type 1 error.......................................................................................................... 261

いType 2 error.......................................................................................................... 261

異常値......................................................................................................................... 293

type()............................................................................................................................45

位置情報.................................................................................................................... 125
一般化線形モデル.............................................................................................. 276
遺伝子座位.............................................................................................................. 125

U

遺伝子発現量行列.............................................................................................. 247

UMAP.................................................................................................. 329, 354, 397

因子負荷量................................................................................................... 307, 311

UPGMA..................................................................................................................... 345

インスタンス......................................................................................................... 107

URL エンコーディング.....................................................................................85

インスタンス化.................................................................................................... 107
インスタンス変数.............................................................................................. 107
インストール............................................................................................................19402

Vインターフェース.............................................................................................. 227

Variable Inspector...............................................................................................30

インデックスファイル................................................................................... 122

venn2()....................................................................................................................... 251

インラインコメント............................................................................................40

独習

Python バイオ情報解析

う偽遺伝子.................................................................................................................... 136

ウォード法.............................................................................................................. 345

キーボードショートカット............................................................................23
機械学習............................................................................................................14, 302
帰無仮説.................................................................................................................... 261

え教師なし学習......................................................................................................... 310

エクソン.................................................................................................................... 135

行マジック.................................................................................................................26

エピゲノム情報.................................................................................................... 285

行ラベル.................................................................................................................... 154

エラー......................................................................................................................... 293

距離行列.................................................................................................................... 362

エラーバー.............................................................................................................. 247

寄与率.............................................................................................................. 307, 316

エントリ.................................................................................................................... 125
くお空間トランスクリプトーム......................................................................... 398

オブジェクト......................................................................................................... 103

クオリティコントロール.............................................................................. 293

オブジェクト指向.............................................................................................. 113

クオリファイア.................................................................................................... 125

オミクス解析......................................................................................................... 285

鎖効果......................................................................................................................... 348
組み込み関数............................................................................................................43
クラス......................................................................................................................... 105

かクラスタ.................................................................................................................... 324

カーネル...............................................................................................................20, 31

クラスタ内分散.................................................................................................... 345

階級............................................................................................................................... 231

クラスタリング.............................................................................. 341, 358, 398

改行コード.................................................................................................................83

クラスタ割り当て.............................................................................................. 359

階層的クラスタリング................................................................................... 342

クロネッカーのデルタ................................................................................... 359

解像度......................................................................................................................... 229
階層ベイズモデリング................................................................................... 369
ガウス分布.............................................................................................................. 260

け過学習......................................................................................................................... 278

経験ベイズ法......................................................................................................... 280

確率的近傍埋め込み......................................................................................... 320

継承............................................................................................................................... 114

確率分布.................................................................................................................... 258

系列データ.............................................................................................................. 242

確率変数.................................................................................................................... 258

ゲノムアセンブリ.............................................................................................. 119

確率密度.................................................................................................................... 258
可視化.............................................................................................................. 223, 283
仮説検定.................................................................................................................... 261

こ片側検定.................................................................................................................... 262

交差エントロピー.............................................................................................. 332

カルバック・ライブラー情報量.............................................................. 321

高次元空間上......................................................................................................... 358

間隔尺度.................................................................................................................... 257

高次元データ......................................................................................................... 284

関数..........................................................................................................................41, 74

合成変数.................................................................................................................... 284

観測値......................................................................................................................... 286

酵母............................................................................................................................... 200
コードセル.................................................................................................................22
コードブロック.......................................................................................................68

きコスト関数.............................................................................................................. 319

キー..................................................................................................................................63

コドン表.................................................................................................................... 135

403

コマンドパレット.................................................................................................25

推定誤差.................................................................................................................... 261

コマンドモード.......................................................................................................22

スコットの選択.................................................................................................... 231

コミュニティ......................................................................................................... 358

裾の重い分布......................................................................................................... 299

コミュニティ検出アルゴリズム.............................................................. 358

スタージェスの公式......................................................................................... 231

コメント.......................................................................................................................40

スチューデントの t 分布................................................................................ 321

混合分布モデル.................................................................................................... 369

スライス............................................................................................................51, 150

コンストラクタ.................................................................................................... 106
せさ

正規化................................................................................................... 232, 298, 393

最尤推定.................................................................................................................... 276

正規表現.......................................................................................................................97

散布図.............................................................................................................. 237, 392

正規分布.................................................................................................................... 260

サンプリング.............................................................................................. 257, 258

制御文字.......................................................................................................................83サンプルサイズ.................................................................................................... 257

セル..................................................................................................................................20

サンプル数.............................................................................................................. 257

セルマジック............................................................................................................27線グラフ.................................................................................................................... 242
潜在変数.................................................................................................................... 284

し選択的推論.............................................................................................................. 282

ジェネレータ関数.............................................................................................. 109

選択的スプライシング................................................................................... 139

シェルコマンド.......................................................................................................28
次元削減......................................................................................................... 305, 396
自作関数.......................................................................................................................74

そ

四捨五入.................................................................................................................... 179

相関係数.................................................................................................................... 267

辞書.......................................................................................................................63, 120

相補鎖変換.............................................................................................................. 116

実験計画.................................................................................................................... 261

ソーシャルグラフ.............................................................................................. 358

四分位点.................................................................................................................... 235

ソート............................................................................................................................54

射影............................................................................................................................... 307

疎行列......................................................................................................................... 289

集合..................................................................................................................................64

属性............................................................................................................................... 107

主座標分析.............................................................................................................. 319
主成分......................................................................................................................... 307
主成分分析................................................................................................... 306, 396

た順序尺度.................................................................................................................... 257

対数化......................................................................................................................... 225

常用対数.................................................................................................................... 178

対数変換.................................................................................................................... 299

初期配置.................................................................................................................... 352

対数尤度.................................................................................................................... 278

シルエット係数.................................................................................................... 357

代表点......................................................................................................................... 352

真偽値......................................................................................................................... 377

対立仮説.................................................................................................................... 261

シングルセル解析................................................................................... 283, 305

多次元尺度構成法.............................................................................................. 319

深層学習.................................................................................................................... 369

多重検定.................................................................................................................... 272
ダッシュボード.......................................................................................................20
タブ区切りテキスト......................................................................................... 287

404

すタプル............................................................................................................................58

推測統計学.............................................................................................................. 257

単位系......................................................................................................................... 302

独習

Python バイオ情報解析

てバイオリンプロット................................................................... 236, 296, 392

テーブルデータ.................................................................................................... 283

バイナリファイル......................................................................................82, 303

テキストファイル.................................................................................................81

バイプロット......................................................................................................... 315

デコレータ.............................................................................................................. 112

破壊的......................................................................................................................... 159

テストセット......................................................................................................... 337

派生クラス.............................................................................................................. 114

転置............................................................................................................................... 157

発現量変動解析.................................................................................................... 279

デンドログラム......................................................................................... 221, 342

バッチラベル......................................................................................................... 389
パラメトリック検定......................................................................................... 262
反復領域.................................................................................................................... 125と凡例............................................................................................................................... 243

遠さ............................................................................................................................... 324
特殊メソッド.............................................................................................. 104, 112
特徴量................................................................................................... 286, 307, 390

ひ特徴量選択.............................................................................................................. 299

ヒートマップ.............................................................................................. 247, 348

特徴量のスケール.............................................................................................. 302

引数............................................................................................................................... 104

度数............................................................................................................................... 231

非計量多次元尺度構成法.............................................................................. 319

度数分布表.............................................................................................................. 231

ヒストグラム......................................................................................................... 231

トピックモデル.................................................................................................... 369

非線形次元削減手法......................................................................................... 329

トランスクリプトーム................................................................................... 284

ビット演算子............................................................................................................94

トレーニングセット......................................................................................... 337

非破壊的.................................................................................................................... 170
非翻訳領域.............................................................................................................. 141
評価関数.................................................................................................................... 352

な評価値............................................................................................................................21

内包表記............................................................................................................73, 121

標準化......................................................................................................................... 302
標準偏差.................................................................................................................... 181
標本............................................................................................................................... 257に比率尺度.................................................................................................................... 257

二項分布.................................................................................................................... 258

ビン数......................................................................................................................... 232のふノイズ.............................................................................................................. 293, 303

ファイル型.................................................................................................................82

ノートブック............................................................................................................20

ファイル形式............................................................................................................81

ノンパラメトリック検定.............................................................................. 262

ファイルの書き込み....................................................................................83, 92
ファイルの読み込み....................................................................................83, 84フィーチャー......................................................................................................... 125

はフィルタリング.............................................................................. 293, 298, 393

バーコード.............................................................................................................. 389

複製開始点.............................................................................................................. 125

パーサー.................................................................................................................... 111

負の二項分布......................................................................................................... 276

パース......................................................................................................................... 111

フラットファイル.............................................................................................. 124

パープレキシティ.............................................................................................. 323

ブロードキャスト................................................................................... 156, 383

バイオインフォマティクス............................................................................14

ブロックコメント.................................................................................................40405

プロット領域......................................................................................................... 226

め

分散............................................................................................................................... 180

名義尺度......................................................................................................... 257, 284

分散安定化.............................................................................................................. 299

メソッド....................................................................................................40, 43, 104

分散共分散行列.................................................................................................... 311

メソッドチェーン...........................................................................44, 117, 177

分散平均比.............................................................................................................. 300

メタ文字.......................................................................................................................97

分子バーコード.................................................................................................... 286
もへモジュラリティ.................................................................................................... 359

ペアプロット......................................................................................................... 241
平均分散プロット.............................................................................................. 238
ベイズ情報量規準.............................................................................................. 358

ゆ平方根......................................................................................................................... 179

有意水準.................................................................................................................... 261

平方根変換.............................................................................................................. 299ユークリッド距離................................................................................... 319, 343

ベルヌーイ試行.................................................................................................... 258

尤度............................................................................................................................... 276

ヘルプ............................................................................................................................26

ユニバーサル関数.............................................................................................. 178

編集モード.................................................................................................................22
ベン図......................................................................................................................... 250
変数..................................................................................................................................44ら
ランダムアクセス.............................................................................................. 120

ほポアソン分布......................................................................................................... 259

り棒グラフ.................................................................................................................... 244

離散値......................................................................................................................... 258

補完..................................................................................................................................25

リスト............................................................................................................................48

母集団......................................................................................................................... 257

両側検定.................................................................................................................... 262

ボックスプロット.............................................................................................. 235

量的データ.............................................................................................................. 231

翻訳............................................................................................................................... 116

隣接行列.................................................................................................................... 363

翻訳領域......................................................................................................... 125, 141る
ま

累積寄与率................................................................................................... 316, 325

マークダウンセル.................................................................................................22
マジックコマンド......................................................................................26, 187
マシンスペック.......................................................................................................14

れ

マスク配列.............................................................................................................. 380

列ラベル.................................................................................................................... 154

マッチオブジェクト......................................................................................... 100

連結............................................................................................................................... 188
連続値......................................................................................................................... 258

む
無名関数.......................................................................................................................57406

独習

Python バイオ情報解析