(Q34408727)

2 August 2017

title

Universal count correction for high-throughput sequencing (English)

1 reference

high-throughput sequencing

2 August 2017

0 references

1 reference

based on heuristic

inferred from title

author name string

Tatsunori B Hashimoto

series ordinal

1

1 reference

2 August 2017

Matthew D Edwards

series ordinal

2

1 reference

2 August 2017

David K Gifford

series ordinal

3

1 reference

2 August 2017

publication date

6 March 2014

1 reference

PLOS Computational Biology

2 August 2017

published in

1 reference

2 August 2017

volume

10

1 reference

2 August 2017

issue

3

1 reference

2 August 2017

page(s)

e1003494

1 reference

Creative Commons Attribution 4.0 International

2 August 2017

copyright license

start time

6 March 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

DESeq2

object named as

DEseq

1 reference

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

cites work

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1 reference

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

6 July 2018

1 reference

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An expansive human regulatory lexicon encoded in transcription factor footprints

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945112

An integrated encyclopedia of DNA elements in the human genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945112

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945112

High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945112

Systematic evaluation of factors influencing ChIP-seq fidelity

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945112

Summarizing and correcting the GC content bias in high-throughput sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945112

A new approach to bias correction in RNA-Seq

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945112

A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945112

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945112

Improving RNA-Seq expression estimates by correcting for fragment bias

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945112

RNA sequencing: advances, challenges and opportunities

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945112

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945112

Differential expression analysis for sequence count data

6 July 2018

1 reference

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A two-parameter generalized Poisson model to improve the analysis of RNA-seq data

6 July 2018

1 reference

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Evaluation of algorithm performance in ChIP-seq peak detection

6 July 2018

1 reference

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Modeling non-uniformity in short-read rates in RNA-Seq data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945112

Biases in Illumina transcriptome sequencing caused by random hexamer priming

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945112

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945112

Computation for ChIP-seq and RNA-seq studies

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945112

BayesPeak: Bayesian analysis of ChIP-seq data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945112

ChIP-seq: advantages and challenges of a maturing technology

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945112

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945112

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945112

RNA-Seq: a revolutionary tool for transcriptomics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945112

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945112

Model-based analysis of ChIP-Seq (MACS)

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945112

High-resolution mapping and characterization of open chromatin across the genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945112

Sequence census methods for functional genomics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945112

Modeling Sage data with a truncated gamma-Poisson model

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3945112

Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture.

6 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003494

10.1371/JOURNAL.PCBI.1003494

21 January 2018

Identifiers

DOI

1 reference

journals/ploscb/HashimotoEG14

2 August 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

2 August 2017

1 reference