cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13534292.v1
title: Additional file 13 of mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes

description: Additional file 13: Table S6. Simulations for expected number of shared alleles (X) for the example dataset- ‘mixexample’. The first row (also the column names) is the number of shared alleles from 0 to 200; and the first column is the index of simulations- 1 to 500. Each row denotes each simulation and shows one distribution of X.
DOI: 10.6084/m9.figshare.13534322.v1
title: Additional file 9 of mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes

description: Additional file 9: Table S2. Table of allele frequency (expected) for example dataset- ‘mixexample’. Each column denotes each marker. The first column lists all alleles appeared at all loci-0, 1, 2, 3, 4, and 5. There is the probability of the allele of this row at the locus of this column.
DOI: 10.6084/m9.figshare.13534292
title: Additional file 13 of mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes

description: Additional file 13: Table S6. Simulations for expected number of shared alleles (X) for the example dataset- ‘mixexample’. The first row (also the column names) is the number of shared alleles from 0 to 200; and the first column is the index of simulations- 1 to 500. Each row denotes each simulation and shows one distribution of X.
DOI: 10.6084/m9.figshare.13534319.v1
title: Additional file 8 of mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes

description: Additional file 8: Table S1. Genotypes of example dataset—‘mixexample’. The raw genotypes of the example data. Each row denotes each individual and each column denotes each marker.
DOI: 10.6084/m9.figshare.13534286
title: Additional file 11 of mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes

description: Additional file 11: Table S4. Table of shared alleles for example dataset- ‘mixexample’. In each cell, the number of shared alleles -0 or 1 or 2, for the pair of individuals of this row at this locus is presented. Column names are markers’ names, and the row names are pairs of individuals.
DOI: 10.6084/m9.figshare.13534283.v1
title: Additional file 10 of mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes

description: Additional file 10: Table S3. Table of heterozygosity for example dataset- ‘mixexample’. In each cell, the status of heterozygosity -0 (homozygous) or 1 (heterozygous), for the individual of this row at this locus is presented. Column names are markers’ names, and the row names are individuals.
DOI: 10.6084/m9.figshare.13549897.v1
title: Additional file 3 of scReQTL: an approach to correlate SNVs to gene expression from individual scRNA-seq datasets

description: Additional file 3.
DOI: 10.6084/m9.figshare.13549900.v1
title: Additional file 4 of scReQTL: an approach to correlate SNVs to gene expression from individual scRNA-seq datasets

description: Additional file 4.
DOI: 10.6084/m9.figshare.13572100.v1
title: Additional file 1 of Current cancer driver variant predictors learn to recognize driver genes instead of functional variants

description: Additional file 1 Zip file containing the datasets used as benchmark in this paper.
DOI: 10.6084/m9.figshare.13572100
title: Additional file 1 of Current cancer driver variant predictors learn to recognize driver genes instead of functional variants

description: Additional file 1 Zip file containing the datasets used as benchmark in this paper.
DOI: 10.6084/m9.figshare.13559923.v1
title: Additional file 2 of Complementary transcriptomic and proteomic analyses reveal the cellular and molecular processes that drive growth and development of Fasciola hepatica in the host liver

description: Additional file 2: Table S1. Gene transcription by F. hepatica 21-day old immature flukes, represented as Fragments per Kilobase of transcript per Million (FPKM).
DOI: 10.6084/m9.figshare.13559923
title: Additional file 2 of Complementary transcriptomic and proteomic analyses reveal the cellular and molecular processes that drive growth and development of Fasciola hepatica in the host liver

description: Additional file 2: Table S1. Gene transcription by F. hepatica 21-day old immature flukes, represented as Fragments per Kilobase of transcript per Million (FPKM).
DOI: 10.6084/m9.figshare.13559935
title: Additional file 6 of Complementary transcriptomic and proteomic analyses reveal the cellular and molecular processes that drive growth and development of Fasciola hepatica in the host liver

description: Additional file 6: Table S4. Identification of proteins within the secretome of F. hepatica 21-day old immature flukes compared with the secretome of NEJ 24 h and adult flukes by LC-MS/MS.
DOI: 10.6084/m9.figshare.13559929.v1
title: Additional file 4 of Complementary transcriptomic and proteomic analyses reveal the cellular and molecular processes that drive growth and development of Fasciola hepatica in the host liver

description: Additional file 4: Table S2. Enrichment of key gene ontology terms within the F. hepatica and F. gigantica immature liver-stage parasite transcriptomes.
DOI: 10.6084/m9.figshare.13559932.v1
title: Additional file 5 of Complementary transcriptomic and proteomic analyses reveal the cellular and molecular processes that drive growth and development of Fasciola hepatica in the host liver

description: Additional file 5: Table S3. Identification of proteins within the somatic proteome of F. hepatica 21-day old immature flukes by LC-MS/MS.
DOI: 10.6084/m9.figshare.13559941
title: Additional file 8 of Complementary transcriptomic and proteomic analyses reveal the cellular and molecular processes that drive growth and development of Fasciola hepatica in the host liver

description: Additional file 8: Table S6. Differential gene expression of genes associated with fibrosis and inflammation, oxidative stress, and proline metabolism within liver tissue of mice infected with F. hepatica. Fold change analysis based on expression of non-infected animals versus mice infected for 21 days, based on data from Rojas-Caraballo et al. [11].
DOI: 10.6084/m9.figshare.13559929
title: Additional file 4 of Complementary transcriptomic and proteomic analyses reveal the cellular and molecular processes that drive growth and development of Fasciola hepatica in the host liver

description: Additional file 4: Table S2. Enrichment of key gene ontology terms within the F. hepatica and F. gigantica immature liver-stage parasite transcriptomes.
DOI: 10.6084/m9.figshare.13559941.v1
title: Additional file 8 of Complementary transcriptomic and proteomic analyses reveal the cellular and molecular processes that drive growth and development of Fasciola hepatica in the host liver

description: Additional file 8: Table S6. Differential gene expression of genes associated with fibrosis and inflammation, oxidative stress, and proline metabolism within liver tissue of mice infected with F. hepatica. Fold change analysis based on expression of non-infected animals versus mice infected for 21 days, based on data from Rojas-Caraballo et al. [11].
DOI: 10.6084/m9.figshare.13559935.v1
title: Additional file 6 of Complementary transcriptomic and proteomic analyses reveal the cellular and molecular processes that drive growth and development of Fasciola hepatica in the host liver

description: Additional file 6: Table S4. Identification of proteins within the secretome of F. hepatica 21-day old immature flukes compared with the secretome of NEJ 24 h and adult flukes by LC-MS/MS.
DOI: 10.6084/m9.figshare.13559932
title: Additional file 5 of Complementary transcriptomic and proteomic analyses reveal the cellular and molecular processes that drive growth and development of Fasciola hepatica in the host liver

description: Additional file 5: Table S3. Identification of proteins within the somatic proteome of F. hepatica 21-day old immature flukes by LC-MS/MS.
DOI: 10.6084/m9.figshare.13572124.v1
title: Additional file 1 of Targetable alterations in invasive pleomorphic lobular carcinoma of the breast

description: Additional file 1: Supplementary Table 1. Clinicopathologic and biomarker status in cases of PLC from TCGA and our institution.
DOI: 10.6084/m9.figshare.13535404.v1
title: Additional file 2 of Chromatin loop anchors contain core structural components of the gene expression machinery in maize

description: Additional file 2. Hi-C replicate 2 TAD-like hierarchical domain coordinates. Categories are the same as in Additional File 1.
DOI: 10.6084/m9.figshare.13535416.v1
title: Additional file 6 of Chromatin loop anchors contain core structural components of the gene expression machinery in maize

description: Additional file 6. ATAC-Seq consensus NF peak coordinates. Coordinates (in bps) and chromosome assignments are shown for all 19,532 consensus NF peaks. (chr) Chromosome assignment; (× 1, × 2) Coordinates in bps of consensus NF peak borders. All coordinates are against the maize B73 AGPv4 assembly.
DOI: 10.6084/m9.figshare.13535419
title: Additional file 7 of Chromatin loop anchors contain core structural components of the gene expression machinery in maize

description: Additional file 7. gene expression data. RNA-Seq were aligned to the maize AGPv4 reference genome and assigned to Gramene gene models for build 4.0 of B73 from the MaizeGDB repository. Genome coordinates and TPM counts for each gene transcripts are shown.
DOI: 10.6084/m9.figshare.13535416
title: Additional file 6 of Chromatin loop anchors contain core structural components of the gene expression machinery in maize

description: Additional file 6. ATAC-Seq consensus NF peak coordinates. Coordinates (in bps) and chromosome assignments are shown for all 19,532 consensus NF peaks. (chr) Chromosome assignment; (× 1, × 2) Coordinates in bps of consensus NF peak borders. All coordinates are against the maize B73 AGPv4 assembly.
DOI: 10.6084/m9.figshare.13572127
title: Additional file 2 of Targetable alterations in invasive pleomorphic lobular carcinoma of the breast

description: Additional file 2: Supplementary Table 2. Molecular alterations in 84 cases of classic ILC from TCGA.
DOI: 10.6084/m9.figshare.13535407
title: Additional file 3 of Chromatin loop anchors contain core structural components of the gene expression machinery in maize

description: Additional file 3. Hi-C replicate 1 chromatin loop coordinates. Coordinates (in bps) and chromosome assignments are shown for both anchors forming a loop. (chr1) Chromosome assignment of first anchor; (× 1, × 2) Coordinates in bps of first anchor; (chr2) Chromosome assignment of second anchor; (y1, y2) Coordinates in bp of second anchor. All coordinates are against the maize B73 AGPv4 assembly.
DOI: 10.6084/m9.figshare.13535401.v1
title: Additional file 1 of Chromatin loop anchors contain core structural components of the gene expression machinery in maize

description: Additional file 1. Hi-C replicate 1 TAD-like hierarchical domain coordinates. (seqid) Chromosomal assignment for domain and sub-domain; (start0) (end0) Coordinates (in bps) of start and end, respectively, of domain or sub-domain; (level) TAD-like domains are denoted as level 0, while sub-domains are denoted as level 1 or higher.
DOI: 10.6084/m9.figshare.13535410
title: Additional file 4 of Chromatin loop anchors contain core structural components of the gene expression machinery in maize

description: Additional file 4. Hi-C replicate 2 chromatin loop coordinates. Coordinates (in bps) and chromosome assignments are shown for both anchors forming a loop. (chr1) Chromosome assignment of first anchor; (× 1, × 2) Coordinates in bps of first anchor; (chr2) Chromosome assignment of second anchor; (y1, y2) Coordinates in bp of second anchor. All coordinates are against the maize B73 AGPv4 assembly.
DOI: 10.6084/m9.figshare.13572127.v1
title: Additional file 2 of Targetable alterations in invasive pleomorphic lobular carcinoma of the breast

description: Additional file 2: Supplementary Table 2. Molecular alterations in 84 cases of classic ILC from TCGA.
DOI: 10.6084/m9.figshare.13535413.v1
title: Additional file 5 of Chromatin loop anchors contain core structural components of the gene expression machinery in maize

description: Additional file 5. ATAC-Seq libraries. Sequencing yields and peak counts are shown for all three biological replicates. All reads were aligned against the maize B73 AGPv4 assembly. Consensus peaks (NF) were used for the study.
DOI: 10.6084/m9.figshare.13535425.v1
title: Additional file 9 of Chromatin loop anchors contain core structural components of the gene expression machinery in maize

description: Additional file 9. replicate 1 chromatin loop anchor annotation and counts for each feature listed below. (seqid) Chromosomal assignment for loop anchor; (start) (end) Coordinates (in bps) of start and end, respectively, of chromatin loop anchor; (locus) name and loop assignment of anchor; (bare) presence or absence of any of the features listed below on anchor (0 = at least one feature present; 1 = no feature present). The following features are annotated: (ef) (uf) expressed (ef) or unexpressed (uf) gene with nearest open chromatin peak &gt;2Kbps away from gene; (en3) (un3) expressed (en3) or unexpressed (un3) gene with nearest open chromatin peak &lt;2Kbps downstream from gene; (en5) (un5) expressed (en5) or unexpressed (un5) gene with nearest open chromatin peak &lt;2Kbps upstream from gene; (eo) (uo) expressed (eo) or unexpressed (uo) gene with nearest open chromatin peak overlapping with gene; (mp) open chromatin peak overlapping an anchor; (mpfe) open chromatin peak overlapping an anchor but with the nearest expressed gene &gt;2Kbps away from the peak.
DOI: 10.6084/m9.figshare.13572124
title: Additional file 1 of Targetable alterations in invasive pleomorphic lobular carcinoma of the breast

description: Additional file 1: Supplementary Table 1. Clinicopathologic and biomarker status in cases of PLC from TCGA and our institution.
DOI: 10.6084/m9.figshare.13535401
title: Additional file 1 of Chromatin loop anchors contain core structural components of the gene expression machinery in maize

description: Additional file 1. Hi-C replicate 1 TAD-like hierarchical domain coordinates. (seqid) Chromosomal assignment for domain and sub-domain; (start0) (end0) Coordinates (in bps) of start and end, respectively, of domain or sub-domain; (level) TAD-like domains are denoted as level 0, while sub-domains are denoted as level 1 or higher.
DOI: 10.6084/m9.figshare.13535410.v1
title: Additional file 4 of Chromatin loop anchors contain core structural components of the gene expression machinery in maize

description: Additional file 4. Hi-C replicate 2 chromatin loop coordinates. Coordinates (in bps) and chromosome assignments are shown for both anchors forming a loop. (chr1) Chromosome assignment of first anchor; (× 1, × 2) Coordinates in bps of first anchor; (chr2) Chromosome assignment of second anchor; (y1, y2) Coordinates in bp of second anchor. All coordinates are against the maize B73 AGPv4 assembly.
DOI: 10.6084/m9.figshare.13535419.v1
title: Additional file 7 of Chromatin loop anchors contain core structural components of the gene expression machinery in maize

description: Additional file 7. gene expression data. RNA-Seq were aligned to the maize AGPv4 reference genome and assigned to Gramene gene models for build 4.0 of B73 from the MaizeGDB repository. Genome coordinates and TPM counts for each gene transcripts are shown.
DOI: 10.6084/m9.figshare.13535407.v1
title: Additional file 3 of Chromatin loop anchors contain core structural components of the gene expression machinery in maize

description: Additional file 3. Hi-C replicate 1 chromatin loop coordinates. Coordinates (in bps) and chromosome assignments are shown for both anchors forming a loop. (chr1) Chromosome assignment of first anchor; (× 1, × 2) Coordinates in bps of first anchor; (chr2) Chromosome assignment of second anchor; (y1, y2) Coordinates in bp of second anchor. All coordinates are against the maize B73 AGPv4 assembly.
DOI: 10.6084/m9.figshare.13535422
title: Additional file 8 of Chromatin loop anchors contain core structural components of the gene expression machinery in maize

description: Additional file 8. overlap analysis of Hi-C replicate 1 and 2 chromatin loop anchors against expressed genes and ATAC-Seq consensus peaks. See Additional File 6 for details. Features overlapping with loop anchors are listed and counted for each Hi-C replicate (“expressed gene”: gene with expression level above expected threshold “unexpressed gene”: gene with expression level below expected threshold; “overlapping peak”: open chromatin peak overlapping with expressed gene; “peak &lt;2Kbps upstream”: open chromatin peak located &lt;2Kbps upstream from expressed gene; “peak &lt;2Kbps downstream”: open chromatin peak located &lt;2Kbps downstream from expressed gene; “peaks &gt;2Kbps”: open chromatin peak located &gt;2Kbps from expressed gene).
DOI: 10.6084/m9.figshare.13535404
title: Additional file 2 of Chromatin loop anchors contain core structural components of the gene expression machinery in maize

description: Additional file 2. Hi-C replicate 2 TAD-like hierarchical domain coordinates. Categories are the same as in Additional File 1.
DOI: 10.6084/m9.figshare.13535422.v1
title: Additional file 8 of Chromatin loop anchors contain core structural components of the gene expression machinery in maize

description: Additional file 8. overlap analysis of Hi-C replicate 1 and 2 chromatin loop anchors against expressed genes and ATAC-Seq consensus peaks. See Additional File 6 for details. Features overlapping with loop anchors are listed and counted for each Hi-C replicate (“expressed gene”: gene with expression level above expected threshold “unexpressed gene”: gene with expression level below expected threshold; “overlapping peak”: open chromatin peak overlapping with expressed gene; “peak &lt;2Kbps upstream”: open chromatin peak located &lt;2Kbps upstream from expressed gene; “peak &lt;2Kbps downstream”: open chromatin peak located &lt;2Kbps downstream from expressed gene; “peaks &gt;2Kbps”: open chromatin peak located &gt;2Kbps from expressed gene).
DOI: 10.6084/m9.figshare.13535425
title: Additional file 9 of Chromatin loop anchors contain core structural components of the gene expression machinery in maize

description: Additional file 9. replicate 1 chromatin loop anchor annotation and counts for each feature listed below. (seqid) Chromosomal assignment for loop anchor; (start) (end) Coordinates (in bps) of start and end, respectively, of chromatin loop anchor; (locus) name and loop assignment of anchor; (bare) presence or absence of any of the features listed below on anchor (0 = at least one feature present; 1 = no feature present). The following features are annotated: (ef) (uf) expressed (ef) or unexpressed (uf) gene with nearest open chromatin peak &gt;2Kbps away from gene; (en3) (un3) expressed (en3) or unexpressed (un3) gene with nearest open chromatin peak &lt;2Kbps downstream from gene; (en5) (un5) expressed (en5) or unexpressed (un5) gene with nearest open chromatin peak &lt;2Kbps upstream from gene; (eo) (uo) expressed (eo) or unexpressed (uo) gene with nearest open chromatin peak overlapping with gene; (mp) open chromatin peak overlapping an anchor; (mpfe) open chromatin peak overlapping an anchor but with the nearest expressed gene &gt;2Kbps away from the peak.
DOI: 10.6084/m9.figshare.13535413
title: Additional file 5 of Chromatin loop anchors contain core structural components of the gene expression machinery in maize

description: Additional file 5. ATAC-Seq libraries. Sequencing yields and peak counts are shown for all three biological replicates. All reads were aligned against the maize B73 AGPv4 assembly. Consensus peaks (NF) were used for the study.
DOI: 10.6084/m9.figshare.13545874.v1
title: Additional file 8 of Predicting chemosensitivity using drug perturbed gene dynamics

description: Additional file 8: Basal Gene Network Analysis presented in Figure 4.
DOI: 10.6084/m9.figshare.13545859.v1
title: Additional file 4 of Predicting chemosensitivity using drug perturbed gene dynamics

description: Additional file 4: Spearman correlations featured in Figure 3.
DOI: 10.6084/m9.figshare.13545862
title: Additional file 5 of Predicting chemosensitivity using drug perturbed gene dynamics

description: Additional file 5: Figure 3 Spearman p-values.
DOI: 10.6084/m9.figshare.13545853
title: Additional file 2 of Predicting chemosensitivity using drug perturbed gene dynamics

description: Additional file 2: Raw Data for Figures 1 and 2.
DOI: 10.6084/m9.figshare.13545871.v1
title: Additional file 7 of Predicting chemosensitivity using drug perturbed gene dynamics

description: Additional file 7: Gene Deltas Network Analysis presented in Figure 4.
DOI: 10.6084/m9.figshare.13545853.v1
title: Additional file 2 of Predicting chemosensitivity using drug perturbed gene dynamics

description: Additional file 2: Raw Data for Figures 1 and 2.
DOI: 10.6084/m9.figshare.13545856.v1
title: Additional file 3 of Predicting chemosensitivity using drug perturbed gene dynamics

description: Additional file 3: Additional Data for Figures 1 and 2.
DOI: 10.6084/m9.figshare.13545856
title: Additional file 3 of Predicting chemosensitivity using drug perturbed gene dynamics

description: Additional file 3: Additional Data for Figures 1 and 2.
DOI: 10.6084/m9.figshare.13545859
title: Additional file 4 of Predicting chemosensitivity using drug perturbed gene dynamics

description: Additional file 4: Spearman correlations featured in Figure 3.
DOI: 10.6084/m9.figshare.13545862.v1
title: Additional file 5 of Predicting chemosensitivity using drug perturbed gene dynamics

description: Additional file 5: Figure 3 Spearman p-values.
DOI: 10.6084/m9.figshare.13545865.v1
title: Additional file 6 of Predicting chemosensitivity using drug perturbed gene dynamics

description: Additional file 6: Maximum absolute differences (MAD) for Figure 3.
DOI: 10.6084/m9.figshare.13545871
title: Additional file 7 of Predicting chemosensitivity using drug perturbed gene dynamics

description: Additional file 7: Gene Deltas Network Analysis presented in Figure 4.
DOI: 10.6084/m9.figshare.13545865
title: Additional file 6 of Predicting chemosensitivity using drug perturbed gene dynamics

description: Additional file 6: Maximum absolute differences (MAD) for Figure 3.
DOI: 10.6084/m9.figshare.13545874
title: Additional file 8 of Predicting chemosensitivity using drug perturbed gene dynamics

description: Additional file 8: Basal Gene Network Analysis presented in Figure 4.
DOI: 10.6084/m9.figshare.13545949
title: Additional file 16 of Transcriptomic time-series analysis of cold- and heat-shock response in psychrotrophic lactic acid bacteria

description: Additional file 16: Table S12. List of motifs with significant E-value discovered based on upstream regions of clustered genes in P. oligofermentans.
DOI: 10.6084/m9.figshare.13545952.v1
title: Additional file 17 of Transcriptomic time-series analysis of cold- and heat-shock response in psychrotrophic lactic acid bacteria

description: Additional file 17: Table S13. List of motifs with significant E-value discovered based on upstream regions of clustered genes in Le. gelidum.
DOI: 10.6084/m9.figshare.13545934.v1
title: Additional file 11 of Transcriptomic time-series analysis of cold- and heat-shock response in psychrotrophic lactic acid bacteria

description: Additional file 11: Table S7. List of genes with a CspA binding site motif in their upstream regions in Le. gelidum, Lc. piscium, and P. oligofermentans.
DOI: 10.6084/m9.figshare.13545952
title: Additional file 17 of Transcriptomic time-series analysis of cold- and heat-shock response in psychrotrophic lactic acid bacteria

description: Additional file 17: Table S13. List of motifs with significant E-value discovered based on upstream regions of clustered genes in Le. gelidum.