(Q39532756)

12 September 2017

Differential peak calling of ChIP-seq signals with replicates with THOR (English)

1 reference

12 September 2017

Manuel Allhoff

1

1 reference

12 September 2017

Kristin Seré

2

1 reference

12 September 2017

Juliana F Pires

3

1 reference

12 September 2017

Martin Zenke

4

1 reference

12 September 2017

Ivan G Costa

5

1 reference

12 September 2017

language of work or name

English

0 references

publication date

2 August 2016

1 reference

12 September 2017

Nucleic Acids Research

1 reference

12 September 2017

44

1 reference

12 September 2017

20

1 reference

12 September 2017

e153

1 reference

Creative Commons Attribution-NonCommercial 4.0 International

12 September 2017

start time

29 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

limma

1 reference

22 June 2022

https://europepmc.org/article/PMC/5175345

based on heuristic

inferred from PubMed Central ID database lookup

cites work

Standardizing chromatin research: a simple and universal method for ChIP-seq.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

Epigenetic program and transcription factor circuitry of dendritic cell development

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

Integrative analysis of 111 reference human epigenomes

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

Enhancer sequence variants and transcription-factor deregulation synergize to construct pathogenic regulatory circuits in B-cell lymphoma

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

limma powers differential expression analyses for RNA-sequencing and microarray studies

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

Analytical tools and current challenges in the modern era of neuroepigenomics

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

Identifying and mitigating bias in next-generation sequencing methods for chromatin biology

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

Immunogenetics. Chromatin state dynamics during blood formation

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

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

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

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

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens.

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

BLUEPRINT: mapping human blood cell epigenomes

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data.

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

Inferring nucleosome positions with their histone mark annotation from ChIP data

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

Human housekeeping genes, revisited

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

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

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

Interpreting noncoding genetic variation in complex traits and human disease

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

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

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

Understanding transcriptional regulation by integrative analysis of transcription factor binding data.

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

An integrated encyclopedia of DNA elements in the human genome

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

Normalization, bias correction, and peak calling for ChIP-seq

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

Detecting differential binding of transcription factors with ChIP-seq

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

Systematic bias in high-throughput sequencing data and its correction by BEADS.

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

Predicting gene expression in T cell differentiation from histone modifications and transcription factor binding affinities by linear mixture models

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

ChIPseqR: analysis of ChIP-seq experiments

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

Differential expression analysis for sequence count data

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

TGF-beta1 accelerates dendritic cell differentiation from common dendritic cell progenitors and directs subset specification toward conventional dendritic cells

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

Evaluation of algorithm performance in ChIP-seq peak detection

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

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

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

GREAT improves functional interpretation of cis-regulatory regions

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

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

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

Histone modification levels are predictive for gene expression

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

Fast and accurate long-read alignment with Burrows-Wheeler transform

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

Computation for ChIP-seq and RNA-seq studies

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

ChIP-seq: advantages and challenges of a maturing technology

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

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

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

Model-based analysis of ChIP-Seq (MACS)

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

Combinatorial patterns of histone acetylations and methylations in the human genome

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

Detecting differential peaks in ChIP-seq signals with ODIN.

13 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

JAMM: a peak finder for joint analysis of NGS replicates

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

Dendritic cell development requires histone deacetylase activity

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

MicroChIP--a rapid micro chromatin immunoprecipitation assay for small cell samples and biopsies

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5175345

An evidence-based approach to identify aging-related genes in Caenorhabditis elegans

21 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKW680

A tutorial on hidden Markov models and selected applications in speech recognition

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKW680

21 January 2018

Identifiers

0 references

1 reference

12 September 2017

PubMed publication ID

27484474

1 reference