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Items: 1 to 20 of 127

1.

MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation.

Gatto L, Lilley KS.

Bioinformatics. 2012 Jan 15;28(2):288-9. doi: 10.1093/bioinformatics/btr645. Epub 2011 Nov 22.

PMID:
22113085
2.

VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants.

Obenchain V, Lawrence M, Carey V, Gogarten S, Shannon P, Morgan M.

Bioinformatics. 2014 Jul 15;30(14):2076-8. doi: 10.1093/bioinformatics/btu168. Epub 2014 Mar 28.

3.

MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments.

Choi M, Chang CY, Clough T, Broudy D, Killeen T, MacLean B, Vitek O.

Bioinformatics. 2014 Sep 1;30(17):2524-6. doi: 10.1093/bioinformatics/btu305. Epub 2014 May 2.

PMID:
24794931
4.

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data.

Morgan M, Anders S, Lawrence M, Aboyoun P, Pagès H, Gentleman R.

Bioinformatics. 2009 Oct 1;25(19):2607-8. doi: 10.1093/bioinformatics/btp450. Epub 2009 Aug 3.

5.

R453Plus1Toolbox: an R/Bioconductor package for analyzing Roche 454 Sequencing data.

Klein HU, Bartenhagen C, Kohlmann A, Grossmann V, Ruckert C, Haferlach T, Dugas M.

Bioinformatics. 2011 Apr 15;27(8):1162-3. doi: 10.1093/bioinformatics/btr102. Epub 2011 Feb 23.

PMID:
21349869
6.

sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments.

Wen B, Xu S, Sheynkman GM, Feng Q, Lin L, Wang Q, Xu X, Wang J, Liu S.

Bioinformatics. 2014 Nov 1;30(21):3136-8. doi: 10.1093/bioinformatics/btu397. Epub 2014 Jul 22.

7.

rTANDEM, an R/Bioconductor package for MS/MS protein identification.

Fournier F, Joly Beauparlant C, Paradis R, Droit A.

Bioinformatics. 2014 Aug 1;30(15):2233-4. doi: 10.1093/bioinformatics/btu178. Epub 2014 Apr 3.

PMID:
24700319
8.

specL--an R/Bioconductor package to prepare peptide spectrum matches for use in targeted proteomics.

Panse C, Trachsel C, Grossmann J, Schlapbach R.

Bioinformatics. 2015 Jul 1;31(13):2228-31. doi: 10.1093/bioinformatics/btv105. Epub 2015 Feb 23.

PMID:
25712692
9.

Visualization of proteomics data using R and bioconductor.

Gatto L, Breckels LM, Naake T, Gibb S.

Proteomics. 2015 Apr;15(8):1375-89. doi: 10.1002/pmic.201400392. Review.

10.

Using R and Bioconductor for proteomics data analysis.

Gatto L, Christoforou A.

Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):42-51. doi: 10.1016/j.bbapap.2013.04.032. Epub 2013 May 18. Review.

PMID:
23692960
11.

The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again.

González-Beltrán A, Neumann S, Maguire E, Sansone SA, Rocca-Serra P.

BMC Bioinformatics. 2014;15 Suppl 1:S11. doi: 10.1186/1471-2105-15-S1-S11. Epub 2014 Jan 10.

12.

A framework for installable external tools in Skyline.

Broudy D, Killeen T, Choi M, Shulman N, Mani DR, Abbatiello SE, Mani D, Ahmad R, Sahu AK, Schilling B, Tamura K, Boss Y, Sharma V, Gibson BW, Carr SA, Vitek O, MacCoss MJ, MacLean B.

Bioinformatics. 2014 Sep 1;30(17):2521-3. doi: 10.1093/bioinformatics/btu148. Epub 2014 May 9.

13.

Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences.

Hon J, Martínek T, Rajdl K, Lexa M.

Bioinformatics. 2013 Aug 1;29(15):1900-1. doi: 10.1093/bioinformatics/btt299. Epub 2013 May 24.

PMID:
23709494
14.

Qupe--a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments.

Albaum SP, Neuweger H, Fränzel B, Lange S, Mertens D, Trötschel C, Wolters D, Kalinowski J, Nattkemper TW, Goesmann A.

Bioinformatics. 2009 Dec 1;25(23):3128-34. doi: 10.1093/bioinformatics/btp568. Epub 2009 Oct 6.

PMID:
19808875
15.

Girafe--an R/Bioconductor package for functional exploration of aligned next-generation sequencing reads.

Toedling J, Ciaudo C, Voinnet O, Heard E, Barillot E.

Bioinformatics. 2010 Nov 15;26(22):2902-3. doi: 10.1093/bioinformatics/btq531. Epub 2010 Sep 21.

16.

DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding.

Chiu TP, Comoglio F, Zhou T, Yang L, Paro R, Rohs R.

Bioinformatics. 2016 Apr 15;32(8):1211-3. doi: 10.1093/bioinformatics/btv735. Epub 2015 Dec 14.

17.

plethy: management of whole body plethysmography data in R.

Bottomly D, Wilmot B, McWeeney SK.

BMC Bioinformatics. 2015 Apr 29;16:134. doi: 10.1186/s12859-015-0547-7.

18.

ProteomeCommons.org IO Framework: reading and writing multiple proteomics data formats.

Falkner JA, Falkner JW, Andrews PC.

Bioinformatics. 2007 Jan 15;23(2):262-3. Epub 2006 Nov 22.

PMID:
17121776
19.

OutlierD: an R package for outlier detection using quantile regression on mass spectrometry data.

Cho H, Kim YJ, Jung HJ, Lee SW, Lee JW.

Bioinformatics. 2008 Mar 15;24(6):882-4. doi: 10.1093/bioinformatics/btn012. Epub 2008 Jan 10.

PMID:
18187441
20.

EasyProt--an easy-to-use graphical platform for proteomics data analysis.

Gluck F, Hoogland C, Antinori P, Robin X, Nikitin F, Zufferey A, Pasquarello C, Fétaud V, Dayon L, Müller M, Lisacek F, Geiser L, Hochstrasser D, Sanchez JC, Scherl A.

J Proteomics. 2013 Feb 21;79:146-60. doi: 10.1016/j.jprot.2012.12.012. Epub 2012 Dec 28.

PMID:
23277275

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