HTSstation: A Web Application and Open-Access Libraries for High-Throughput Sequencing Data Analysis

被引：60

作者：

David, Fabrice P. A. ^{[1
,2
]}

Delafontaine, Julien ^{[1
,2
]}

Carat, Solenne ^{[1
,2
]}

Ross, Frederick J. ^{[1
,2
]}

Lefebvre, Gregory ^{[1
,2
]}

Jarosz, Yohan ^{[1
,2
]}

Sinclair, Lucas ^{[1
,2
]}

Noordermeer, Daan ^{[1
,3
]}

Rougemont, Jacques ^{[1
,2
]}

Leleu, Marion ^{[1
,2
,3
]}

机构：

[1] Ecole Polytech Fed Lausanne, Sch Life Sci, CH-1015 Lausanne, Switzerland

[2] SIB, Lausanne, Switzerland

[3] ISREC, Lausanne, Switzerland

来源：

PLOS ONE | 2014年 / 9卷 / 01期

基金：

瑞士国家科学基金会;

关键词：

CHIP-SEQ DATA; CONFORMATION; GENOME; TOOLS; SUITE;

D O I：

10.1371/journal.pone.0085879

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

The HTSstation analysis portal is a suite of simple web forms coupled to modular analysis pipelines for various applications of High-Throughput Sequencing including ChIP-seq, RNA-seq, 4C-seq and re-sequencing. HTSstation offers biologists the possibility to rapidly investigate their HTS data using an intuitive web application with heuristically pre-defined parameters. A number of open-source software components have been implemented and can be used to build, configure and run HTS analysis pipelines reactively. Besides, our programming framework empowers developers with the possibility to design their own workflows and integrate additional third-party software. The HTSstation web application is accessible at http://htsstation.epfl.ch.

引用

页数：9

共 33 条

[1] Improved scoring of functional groups from gene expression data by decorrelating GO graph structure [J].

Alexa, Adrian ;

Rahnenfuehrer, Joerg ;

Lengauer, Thomas .

BIOINFORMATICS, 2006, 22 (13) :1600-1607

[2]

Anders S., 2010, GENOME BIOL, V11, pR106, DOI [10.1186/gb-2010-11-10-r106, DOI 10.1186/gb-2010-11-10-r106]

[3] A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs [J].

Andrey, Guillaume ;

Montavon, Thomas ;

Mascrez, Benedicte ;

Gonzalez, Federico ;

Noordermeer, Daan ;

Leleu, Marion ;

Trono, Didier ;

Spitz, Francois ;

Duboule, Denis .

SCIENCE, 2013, 340 (6137) :1195-+

[4] MEME SUITE: tools for motif discovery and searching [J].

Bailey, Timothy L. ;

Boden, Mikael ;

Buske, Fabian A. ;

Frith, Martin ;

Grant, Charles E. ;

Clementi, Luca ;

Ren, Jingyuan ;

Li, Wilfred W. ;

Noble, William S. .

NUCLEIC ACIDS RESEARCH, 2009, 37 :W202-W208

[5] Global chromatin domain organization of the Drosophila genome [J].

de Wit, Elzo ;

Braunschweig, Ulrich ;

Greil, Frauke ;

Bussemaker, Harmen J. ;

van Steensel, Bas .

PLOS GENETICS, 2008, 4 (03)

[6] Ensembl 2013 [J].

Flicek, Paul ;

Ahmed, Ikhlak ;

Amode, M. Ridwan ;

Barrell, Daniel ;

Beal, Kathryn ;

Brent, Simon ;

Carvalho-Silva, Denise ;

Clapham, Peter ;

Coates, Guy ;

Fairley, Susan ;

Fitzgerald, Stephen ;

Gil, Laurent ;

Garcia-Giron, Carlos ;

Gordon, Leo ;

Hourlier, Thibaut ;

Hunt, Sarah ;

Juettemann, Thomas ;

Kaehaeri, Andreas K. ;

Keenan, Stephen ;

Komorowska, Monika ;

Kulesha, Eugene ;

Longden, Ian ;

Maurel, Thomas ;

McLaren, William M. ;

Muffato, Matthieu ;

Nag, Rishi ;

Overduin, Bert ;

Pignatelli, Miguel ;

Pritchard, Bethan ;

Pritchard, Emily ;

Riat, Harpreet Singh ;

Ritchie, Graham R. S. ;

Ruffier, Magali ;

Schuster, Michael ;

Sheppard, Daniel ;

Sobral, Daniel ;

Taylor, Kieron ;

Thormann, Anja ;

Trevanion, Stephen ;

White, Simon ;

Wilder, Steven P. ;

Aken, Bronwen L. ;

Birney, Ewan ;

Cunningham, Fiona ;

Dunham, Ian ;

Harrow, Jennifer ;

Herrero, Javier ;

Hubbard, Tim J. P. ;

Johnson, Nathan ;

Kinsella, Rhoda .

NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) :D48-D55

[7]

Gheldof N, 2012, METHODS MOL BIOL, V786, P211, DOI 10.1007/978-1-61779-292-2_13

[8] Galaxy: A platform for interactive large-scale genome analysis [J].

Giardine, B ;

Riemer, C ;

Hardison, RC ;

Burhans, R ;

Elnitski, L ;

Shah, P ;

Zhang, Y ;

Blankenberg, D ;

Albert, I ;

Taylor, J ;

Miller, W ;

Kent, WJ ;

Nekrutenko, A .

GENOME RESEARCH, 2005, 15 (10) :1451-1455

[9] GeneProf: analysis of high-throughput sequencing experiments [J].

Halbritter, Florian ;

Vaidya, Harsh J. ;

Tomlinson, Simon R. .

NATURE METHODS, 2012, 9 (01) :7-8

[10]

Huang Songbo, 2011, Frontiers in Genetics, V2, P46, DOI 10.3389/fgene.2011.00046

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