Package: genemunge
Tools for munging genomic data such as: - Converting between different
types of gene identifiers - Searching for terms in the Gene Ontology
(GO) associated with a keyword - Looking up housekeeping genes and
transcription factors - Getting a list of GO terms associated with a
given gene - Looking up how a gene is expressed across tissues -
Normalizing a matrix of gene expression data by converting to TPMUnlearn.AIWhen we’re not developing super awesome open source packages likegenemunge, we help biopharma partners use unsupervised deep learning
to extract insights from their omics data. Learn more atunlearn.health.InstallThis library is accompanied by the following data sources: - TheGene
Ontology. The current version used here is
the 2018-03-27 release. -recount2data for
GTEx. -HGNCgene symbols. - A list oftranscription factors. - A list ofhousekeeping genes.Installing this package throughpip(pip install genemungefrom PyPI,pip install .from GitHub) will use the static data that accompanies this repository.If you wish to use the latest data from the above sources, you may
install in “develop” mode from GitHub withpip-einstall .. Notably, this will
download and process the recount2 GTEx data, requiringRand therecountpackage frombioconductor:source("https://bioconductor.org/biocLite.R")
biocLite("recount")CitationsPlease cite the following papers if you make use of genemunge for a
publication.This package:Gene Ontology: Ashburner et al. Gene ontology: tool for the unification
of biology (2000) Nat Genet 25(1):25-9 GO Consortium, Nucleic Acids
Res., 2017recount2: Collado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA,
Hansen KD, Jaffe AE, Langmead B, Leek JT. Reproducible RNA-seq analysis
using recount2. Nature Biotechnology, 2017.HGNC: Gray KA, Yates B, Seal RL, Wright MW, Bruford EA. genenames.org:
the HGNC resources in 2015. Nucleic Acids Res. 2015 Jan;43(Database
issue):D1079-85.Transcription factors: TFcheckpoint: a curated compendium of specific
DNA-binding RNA polymerase II transcription factors Konika Chawla;
Sushil Tripathi; Liv Thommesen; Astrid Laegreid; Martin Kuiper
Bioinformatics 2013.Housekeeping genes: E. Eisenberg and E.Y. Levanon, Trends in Genetics
29, (2013)Similar toolsIf you know of similar tools that would be helpful references for users,
please contribute an attribution to them here.goatoolsgoenrichGO evidence codesExperiment:
 - Inferred from Experiment (EXP)
 - Inferred from Direct Assay (IDA)
 - Inferred from Physical Interaction (IPI)
 - Inferred from Mutant Phenotype (IMP)
 - Inferred from Genetic Interaction (IGI)
 - Inferred from Expression Pattern (IEP)

Computational:
 - Inferred from Sequence or structural Similarity (ISS)
 - Inferred from Sequence Orthology (ISO)
 - Inferred from Sequence Alignment (ISA)
 - Inferred from Sequence Model (ISM)
 - Inferred from Genomic Context (IGC)
 - Inferred from Biological aspect of Ancestor (IBA)
 - Inferred from Biological aspect of Descendant (IBD)
 - Inferred from Key Residues (IKR)
 - Inferred from Rapid Divergence(IRD)
 - Inferred from Reviewed Computational Analysis (RCA)

Literature:
 - Traceable Author Statement (TAS)
 - Non-traceable Author Statement (NAS)

Other:
 - Inferred by Curator (IC)
 - No biological Data available (ND) evidence code
 - Inferred from Electronic Annotation (IEA)Common gene id types['symbol','name','entrez_id','ensembl_gene_id','refseq_accession','uniprot_ids']