(Q31042116)

14 October 2017

From reads to regions: a Bioconductor workflow to detect differential binding in ChIP-seq data (English)

1 reference

14 October 2017

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2

1 reference

14 October 2017

Aaron T L Lun

1

1 reference

PMC publication ID

4706055

14 October 2017

language of work or name

1 reference

16 October 2015

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14 October 2017

1 reference

14 October 2017

4

1 reference

14 October 2017

1080

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Creative Commons Attribution 4.0 International

14 October 2017

start time

11 January 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

edgeR

object named as

edgeR

1 reference

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

cites work

csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706055

Orchestrating high-throughput genomic analysis with Bioconductor

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706055

The UCSC Genome Browser database: 2015 update

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706055

Genome-wide and single-cell analyses reveal a context dependent relationship between CBP recruitment and 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=4706055

De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706055

MMDiff: quantitative testing for shape changes in ChIP-Seq data sets

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706055

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706055

Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706055

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706055

An integrated encyclopedia of DNA elements 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=4706055

H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706055

The B-cell identity factor Pax5 regulates distinct transcriptional programmes in early and late B lymphopoiesis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706055

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706055

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706055

Detecting differential binding of transcription factors with ChIP-seq

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706055

ChIPseqR: analysis of ChIP-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=4706055

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706055

A scaling normalization method for differential expression analysis of RNA-seq data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706055

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706055

rtracklayer: an R package for interfacing with genome browsers

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706055

Design and analysis of ChIP-seq experiments for DNA-binding proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706055

Model-based analysis of ChIP-Seq (MACS)

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706055

Changes in gene expression profiles in developing B cells of murine bone marrow

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706055

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4706055

Faster cyclic loess: normalizing RNA arrays via linear models.

21 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.12688%2FF1000RESEARCH.7016.2

Global changes in the mammary epigenome are induced by hormonal cues and coordinated by Ezh2.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.12688%2FF1000RESEARCH.7016.2

An improved Bonferroni procedure for multiple tests of significance

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.12688%2FF1000RESEARCH.7016.2

Selective Regulation of Mature IgG1 Transcription by CD86 and β2-Adrenergic Receptor Stimulation

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26834993

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.12688/F1000RESEARCH.7016.2

1 reference

14 October 2017

1 reference

PMC publication ID

4706055

14 October 2017

PubMed publication ID

26834993

1 reference

PMC publication ID

4706055