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

被引：45

作者：

Planet, Evarist ^{[1
]}

Stephan-Otto Attolini, Camille ^{[1
]}

Reina, Oscar ^{[1
]}

Flores, Oscar ^{[2
]}

Rossell, David ^{[1
]}

机构：

[1] Inst Res Biomed Barcelona, Biostat & Bioinformat Unit, Barcelona, Spain

[2] IRB Barcelona, IRB BSC Joint Res Program Computat Biol, Barcelona, Spain

来源：

BIOINFORMATICS | 2012年 / 28卷 / 04期

关键词：

D O I：

10.1093/bioinformatics/btr700

中图分类号：

Q5 [生物化学];

学科分类号：

070307 [化学生物学];

摘要：

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 immunoprecipitation and overamplification artifacts, de novo identification of read- rich genomic regions and visualization of the location and coverage of genomic region lists.

引用

页码：589 / 590

页数：2

共 5 条

[1]

[Anonymous], 1912, Variabilita e Mutuabilita. Contributo allo Studio delle Distribuzioni e delle Relazioni Statistiche

[2]

Empirical Bayes analysis of a microarray experiment [J].

Efron, B ;

Tibshirani, R ;

Storey, JD ;

Tusher, V .

JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, 2001, 96 (456) :1151-1160

[3]

Bioconductor: open software development for computational biology and bioinformatics [J].

Gentleman, RC ;

Carey, VJ ;

Bates, DM ;

Bolstad, B ;

Dettling, M ;

Dudoit, S ;

Ellis, B ;

Gautier, L ;

Ge, YC ;

Gentry, J ;

Hornik, K ;

Hothorn, T ;

Huber, W ;

Iacus, S ;

Irizarry, R ;

Leisch, F ;

Li, C ;

Maechler, M ;

Rossini, AJ ;

Sawitzki, G ;

Smith, C ;

Smyth, G ;

Tierney, L ;

Yang, JYH ;

Zhang, JH .

GENOME BIOLOGY, 2004, 5 (10)

[4]

ESTIMATING DIMENSION OF A MODEL [J].

SCHWARZ, G .

ANNALS OF STATISTICS, 1978, 6 (02) :461-464

[5]

Zhang Y., 2008, GENOME BIOL, V9, pR173

← 1 →