TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages (Q31165459)

21 August 2017

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages (English)

1 reference

21 August 2017

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13 June 2020

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13 June 2020

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28232861%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

Tiago C Silva

1 reference

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13 June 2020

Catharina Olsen

series ordinal

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13 June 2020

Michele Ceccarelli

series ordinal

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13 June 2020

Houtan Noushmehr

series ordinal

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13 June 2020

publication date

29 June 2016

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21 August 2017

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13 June 2020

volume

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13 June 2020

page(s)

1542

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Creative Commons Attribution 4.0 International

13 June 2020

start time

28 December 2016

1 reference

April 2022 Public Data File from Crossref

copyrighted

0 references

describes a project that uses

1 reference

10 June 2022

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&rettype=xml&id=5302158

ComplexHeatmap

object named as

ComplexHeatmap

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

edgeR

object named as

edgeR

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

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21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

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21 June 2018

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A large genomic deletion leads to enhancer adoption by the lamin B1 gene: a second path to autosomal dominant adult-onset demyelinating leukodystrophy (ADLD)

21 June 2018

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Integrative analysis of 111 reference human epigenomes

21 June 2018

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21 June 2018

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Comprehensive genomic characterization of head and neck squamous cell carcinomas

21 June 2018

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Integrated genomic characterization of papillary thyroid carcinoma

21 June 2018

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The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data

21 June 2018

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RTCGAToolbox: a new tool for exporting TCGA Firehose data

21 June 2018

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The somatic genomic landscape of chromophobe renal cell carcinoma

21 June 2018

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Comprehensive molecular profiling of lung adenocarcinoma

21 June 2018

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Comprehensive molecular characterization of gastric adenocarcinoma

21 June 2018

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A single oncogenic enhancer rearrangement causes concomitant EVI1 and GATA2 deregulation in leukemia

21 June 2018

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Integrative analysis of high-throughput cancer studies with contrasted penalization

21 June 2018

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21 June 2018

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Comprehensive molecular characterization of clear cell renal cell carcinoma

21 June 2018

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Pathview: an R/Bioconductor package for pathway-based data integration and visualization

21 June 2018

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An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform

21 June 2018

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Comprehensive molecular portraits of human breast tumours

21 June 2018

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Comprehensive genomic characterization of squamous cell lung cancers

21 June 2018

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Comprehensive molecular characterization of human colon and rectal cancer

21 June 2018

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21 June 2018

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CpG islands and the regulation of transcription

21 June 2018

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GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

21 June 2018

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21 June 2018

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Statistical approaches for the analysis of DNA methylation microarray data

21 June 2018

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An integrated pipeline for the genome-wide analysis of transcription factor binding sites from ChIP-Seq.

21 June 2018

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A unique chromatin signature uncovers early developmental enhancers in humans

21 June 2018

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Histone H3K27ac separates active from poised enhancers and predicts developmental state

21 June 2018

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NCBI Epigenomics: a new public resource for exploring epigenomic data sets

21 June 2018

1 reference

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Molecular Signals of Epigenetic States

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5302158

The NIH Roadmap Epigenomics Mapping Consortium

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5302158

GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5302158

Inferring the conservative causal core of gene regulatory networks

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5302158

Next-generation genomics: an integrative approach

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5302158

Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5302158

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5302158

The landscape of somatic copy-number alteration across human cancers

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5302158

Histone modifications at human enhancers reflect global cell-type-specific gene expression

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5302158

GADEM: a genetic algorithm guided formation of spaced dyads coupled with an EM algorithm for motif discovery

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5302158

minet: A R/Bioconductor package for inferring large transcriptional networks using mutual information

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5302158

Information-theoretic inference of large transcriptional regulatory networks.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5302158

Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5302158

STAMP: a web tool for exploring DNA-binding motif similarities

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5302158

DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5302158

Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5302158

Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5302158

ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5302158

BioGRID: a general repository for interaction datasets

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5302158

DNA methylation and human disease

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5302158

Integrative analysis of the cancer transcriptome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5302158

Genomic maps and comparative analysis of histone modifications in human and mouse

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5302158

Partitioning and plasticity of repressive histone methylation states in mammalian chromatin

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5302158

Mice lacking a Myc enhancer that includes human SNP rs6983267 are resistant to intestinal tumors.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5302158

Histone H3 acetylated at lysine 9 in promoter is associated with low nucleosome density in the vicinity of transcription start site in human cell

31 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28232861

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.12688/F1000RESEARCH.8923.2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28232861%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28232861%20AND%20SRC:MED&resulttype=core&format=json

13 June 2020

PubMed publication ID

28232861

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28232861%20AND%20SRC:MED&resulttype=core&format=json