ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline (Q36156400)

12 August 2017

ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline (English)

1 reference

12 August 2017

0 references

14

1 reference

12 August 2017

Tao Liu

9

0 references

Chongzhi Zang

object named as

Chongzhi Zang

10

0 references

Myles Brown

15

object named as

Myles Brown

1 reference

12 August 2017

Qian Qin

1

1 reference

12 August 2017

Shenglin Mei

2

1 reference

12 August 2017

Qiu Wu

3

1 reference

12 August 2017

Hanfei Sun

4

1 reference

12 August 2017

Lewyn Li

5

1 reference

12 August 2017

Len Taing

6

1 reference

12 August 2017

Sujun Chen

7

1 reference

12 August 2017

Fugen Li

8

1 reference

12 August 2017

Han Xu

11

1 reference

12 August 2017

Yiwen Chen

12

1 reference

12 August 2017

Clifford A Meyer

13

1 reference

12 August 2017

Henry W Long

16

1 reference

12 August 2017

X Shirley Liu

17

1 reference

12 August 2017

3 October 2016

1 reference

12 August 2017

1 reference

12 August 2017

17

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12 August 2017

1

1 reference

12 August 2017

404

1 reference

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization.

12 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

Large-scale quality analysis of published ChIP-seq data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

Target analysis by integration of transcriptome and ChIP-seq data with BETA.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

The mutational landscape of chromatin regulatory factors across 4,623 tumor samples

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

A quality control system for profiles obtained by ChIP sequencing.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

Predicting the molecular complexity of sequencing libraries

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

FoxA1 specifies unique androgen and glucocorticoid receptor binding events in prostate cancer cells.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

STAR: ultrafast universal RNA-seq aligner

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

CHANCE: comprehensive software for quality control and validation of ChIP-seq data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

The accessible chromatin landscape of the human genome

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

An integrated encyclopedia of DNA elements in the human genome

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

Systematic evaluation of factors influencing ChIP-seq fidelity

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

HIstome--a relational knowledgebase of human histone proteins and histone modifying enzymes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

Fish the ChIPs: a pipeline for automated genomic annotation of ChIP-Seq data.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

Dual role of FoxA1 in androgen receptor binding to chromatin, androgen signalling and prostate cancer

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

Cistrome: an integrative platform for transcriptional regulation studies

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

An integrated ChIP-seq analysis platform with customizable workflows

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

Sox2 cooperates with Chd7 to regulate genes that are mutated in human syndromes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

The distal V(H) gene cluster of the Igh locus contains distinct regulatory elements with Pax5 transcription factor-dependent activity in pro-B cells

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

seqMINER: an integrated ChIP-seq data interpretation platform

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

BigWig and BigBed: enabling browsing of large distributed datasets

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

The in vivo pattern of binding of RAG1 and RAG2 to antigen receptor loci.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

Distinct factors control histone variant H3.3 localization at specific genomic regions

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

The Sequence Alignment/Map format and SAMtools

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

Fast and accurate short read alignment with Burrows-Wheeler transform

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

TFCat: the curated catalog of mouse and human transcription factors

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

A census of human transcription factors: function, expression and evolution

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

An integrated software system for analyzing ChIP-chip and ChIP-seq data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

An RNAi screen of chromatin proteins identifies Tip60-p400 as a regulator of embryonic stem cell identity.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

htSeqTools: high-throughput sequencing quality control, processing and visualization in R.

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

Genome-wide profiling of interleukin-4 and STAT6 transcription factor regulation of human Th2 cell programming.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5048594

10.1186/S12859-016-1274-4

23 September 2018

Identifiers

DOI

1 reference

journals/bmcbi/QinMWSLTCLLZXCM16

12 August 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

12 August 2017

PubMed publication ID

27716038

1 reference