PePr: a peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data. (Q30828757)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24894502%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

title

PePr: a peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24894502%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

1 reference

1 reference

1

1 reference

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19 March 2020

Maureen Sartor

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24894502%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

author name string

Yu-Hsuan Lin

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24894502%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

Timothy D Johnson

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24894502%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

Laura S Rozek

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24894502%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

language of work or name

English

0 references

publication date

3 June 2014

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24894502%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

number of pages

8

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based on heuristic

inferred from page(s)

published in

Bioinformatics

1 reference

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19 March 2020

volume

30

1 reference

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19 March 2020

issue

18

1 reference

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19 March 2020

page(s)

2568-2575

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24894502%20AND%20SRC:MED&resulttype=core&format=json

Targeting the epigenome in lung cancer: expanding approaches to epigenetic therapy

19 March 2020

cites work

1 reference

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Functions, aberrations, and advances for chromatin modulation in cancer

21 June 2018

1 reference

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diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155259

ER-stress-induced transcriptional regulation increases protein synthesis leading to cell death.

21 June 2018

1 reference

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Differential analysis of gene regulation at transcript resolution with RNA-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=4155259

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=4155259

An integrated encyclopedia of DNA elements in the human genome

21 June 2018

1 reference

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Functional analysis of transcription factor binding sites in human promoters

21 June 2018

1 reference

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The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding

21 June 2018

1 reference

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

21 June 2018

1 reference

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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=4155259

ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155259

Genome-wide methylation and expression differences in HPV(+) and HPV(-) squamous cell carcinoma cell lines are consistent with divergent mechanisms of carcinogenesis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155259

FIMO: scanning for occurrences of a given motif

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155259

Identifying dispersed epigenomic domains from ChIP-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=4155259

A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155259

Differential expression analysis for sequence count 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=4155259

HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-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=4155259

Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155259

Distinct histone modifications in stem cell lines and tissue lineages from the early mouse embryo

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155259

A signal-noise model for significance analysis of ChIP-seq with negative control

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155259

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=4155259

Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-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=4155259

Human papillomavirus in head and neck cancer: its role in pathogenesis and clinical implications

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155259

Computation for ChIP-seq and RNA-seq studies

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155259

ChIP-seq: advantages and challenges of a maturing technology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155259

A clustering approach for identification of enriched domains from histone modification ChIP-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=4155259

Fast and accurate short read alignment with Burrows-Wheeler transform

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155259

Genome-wide analysis of transcription factor binding sites based on ChIP-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=4155259

Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155259

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155259

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=4155259

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=4155259

F-Seq: a feature density estimator for high-throughput sequence tags

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155259

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-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=4155259

FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155259

Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray 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=4155259

Linear models and empirical bayes methods for assessing differential expression in microarray 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=4155259

Dynamic alterations of specific histone modifications during early murine development

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155259

Java Treeview--extensible visualization of microarray 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=4155259

Fitting a mixture model by expectation maximization to discover motifs in biopolymers

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155259

BroadPeak: a novel algorithm for identifying broad peaks in diffuse ChIP-seq datasets.

21 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTU372

10.1093/BIOINFORMATICS/BTU372

21 January 2018

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24894502%20AND%20SRC:MED&resulttype=core&format=json

journals/bioinformatics/ZhangLJRS14

19 March 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24894502%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

PubMed publication ID

24894502

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24894502%20AND%20SRC:MED&resulttype=core&format=json