PolyaPeak: detecting transcription factor binding sites from ChIP-seq using peak shape information (Q35114443)

6 August 2017

PolyaPeak: detecting transcription factor binding sites from ChIP-seq using peak shape information (English)

1 reference

6 August 2017

Hao Wu

1

1 reference

PubMed ID

24608116

6 August 2017

Hongkai Ji

series ordinal

2

1 reference

PubMed ID

24608116

6 August 2017

language of work or name

English

0 references

publication date

7 March 2014

1 reference

6 August 2017

1 reference

6 August 2017

9

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6 August 2017

3

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6 August 2017

e89694

1 reference

Creative Commons Attribution 4.0 International

6 August 2017

start time

7 March 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

A Statistical Framework for the Analysis of ChIP-Seq Data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3946423

hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data

9 July 2018

1 reference

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Shape-based peak identification for ChIP-Seq

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3946423

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

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3946423

Discovering homotypic binding events at high spatial resolution.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3946423

MM Algorithms for Some Discrete Multivariate Distributions.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3946423

Evaluation of algorithm performance in ChIP-seq peak detection

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3946423

HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3946423

A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3946423

BayesPeak: Bayesian analysis of ChIP-seq data

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3946423

Unlocking the secrets of the genome

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3946423

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

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3946423

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

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3946423

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

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3946423

Model-based analysis of ChIP-Seq (MACS)

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3946423

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3946423

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

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3946423

Integration of external signaling pathways with the core transcriptional network in embryonic stem cells

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3946423

Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3946423

Genome-wide mapping of in vivo protein-DNA interactions

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3946423

The ENCODE Project at UC Santa Cruz

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3946423

TRANSFAC: transcriptional regulation, from patterns to profiles

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3946423

PICS: probabilistic inference for ChIP-seq.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3946423

10.1371/JOURNAL.PONE.0089694

27 September 2018

Identifiers

DOI

1 reference

6 August 2017

0 references

1 reference

6 August 2017

1 reference

PubMed ID

24608116