Literature DB >> 22199381

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

Evarist Planet1, Camille Stephan-Otto Attolini, Oscar Reina, Oscar Flores, David Rossell.   

Abstract

UNLABELLED: We provide a Bioconductor package with quality assessment, processing and visualization tools for high-throughput sequencing data, with emphasis in ChIP-seq and RNA-seq studies. It includes detection of outliers and biases, inefficient immuno-precipitation and overamplification artifacts, de novo identification of read-rich genomic regions and visualization of the location and coverage of genomic region lists. AVAILABILITY: www.bioconductor.org.

Mesh：

Year:  2011        PMID： 22199381     DOI： 10.1093/bioinformatics/btr700

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  30 in total

1.  Differential expression of human tRNA genes drives the abundance of tRNA-derived fragments.

Authors:  Adrian Gabriel Torres; Oscar Reina; Camille Stephan-Otto Attolini; Lluís Ribas de Pouplana
Journal:  Proc Natl Acad Sci U S A       Date:  2019-04-08       Impact factor: 11.205

Review 2.  From next-generation resequencing reads to a high-quality variant data set.

Authors:  S P Pfeifer
Journal:  Heredity (Edinb)       Date:  2016-10-19       Impact factor: 3.821

3.  Data exploration, quality control and statistical analysis of ChIP-exo/nexus experiments.

Authors:  Rene Welch; Dongjun Chung; Jeffrey Grass; Robert Landick; Sündüz Keles
Journal:  Nucleic Acids Res       Date:  2017-09-06       Impact factor: 16.971

4.  The fission yeast CENP-B protein Abp1 prevents pervasive transcription of repetitive DNA elements.

Authors:  Anne Daulny; Eva Mejía-Ramírez; Oscar Reina; Jesus Rosado-Lugo; Lorena Aguilar-Arnal; Herbert Auer; Mikel Zaratiegui; Fernando Azorin
Journal:  Biochim Biophys Acta       Date:  2016-06-23

5.  BSeQC: quality control of bisulfite sequencing experiments.

Authors:  Xueqiu Lin; Deqiang Sun; Benjamin Rodriguez; Qian Zhao; Hanfei Sun; Yong Zhang; Wei Li
Journal:  Bioinformatics       Date:  2013-09-23       Impact factor: 6.937

6.  Decoding human gene expression signatures in the brain.

Authors:  Guang-Zhong Wang; Genevieve Konopka
Journal:  Transcription       Date:  2013-05-01

Review 7.  Identifying and mitigating bias in next-generation sequencing methods for chromatin biology.

Authors:  Clifford A Meyer; X Shirley Liu
Journal:  Nat Rev Genet       Date:  2014-09-16       Impact factor: 53.242

Review 8.  Genomics of alternative splicing: evolution, development and pathophysiology.

Authors:  Eric R Gamazon; Barbara E Stranger
Journal:  Hum Genet       Date:  2014-01-01       Impact factor: 4.132

9.  Circadian- and UPR-dependent control of CPEB4 mediates a translational response to counteract hepatic steatosis under ER stress.

Authors:  Carlos Maillo; Judit Martín; David Sebastián; Maribel Hernández-Alvarez; Mar García-Rocha; Oscar Reina; Antonio Zorzano; Mercedes Fernandez; Raúl Méndez
Journal:  Nat Cell Biol       Date:  2017-01-16       Impact factor: 28.824

10.  dKDM5/LID regulates H3K4me3 dynamics at the transcription-start site (TSS) of actively transcribed developmental genes.

Authors:  Marta Lloret-Llinares; Sílvia Pérez-Lluch; David Rossell; Tomás Morán; Joan Ponsa-Cobas; Herbert Auer; Montserrat Corominas; Fernando Azorín
Journal:  Nucleic Acids Res       Date:  2012-08-16       Impact factor: 16.971
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