MSnbase 2.19.1 – Base Functions and Classes for MS-based Proteomics

MSnbase 2.19.1

:: DESCRIPTION

MSnbase is an R/Bioconductor package for the analysis of quantitative proteomics experiments that use isobaric tagging. It provides an exploratory data analysis framework for reproducible research, allowing raw data import, quality control, visualization, data processing and quantitation.

::DEVELOPER

Dr Laurent Gatto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
R
Bioconductor

:: DOWNLOAD

MSnbase

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jan 15;28(2):288-9. doi: 10.1093/bioinformatics/btr645. Epub 2011 Nov 22.
MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation.
Gatto L, Lilley KS.

ShortRead 1.42.0 – Classes and Methods for High-throughput Short-read Sequencing data

ShortRead 1.42.0

:: DESCRIPTION

ShortRead is a package for input, quality assessment, manipulation and output of high-throughput sequencing data.

:: DEVELOPER

ShortRead team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Mac OsX/Windows
R package
BioConductor

:: DOWNLOAD

ShortRead

:: MORE INFORMATION

Citation

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

CLASS 2.1.7 – Constraint-based Local Assembly and Selection of Splice Variants

CLASS 2.1.7

:: DESCRIPTION

CLASS is a software tool for accurately assembling splice variants using local read coverage patterns of RNA-seq reads, contiguity constraints from read pairs and spliced reads, and optionally information about gene structure extracted from cDNA sequence databases.

::DEVELOPER

Li Song

:: SCREENSHOTS

N/A

:: REQUIREMENTS

MacOsx/Linux

:: DOWNLOAD

CLASS

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013;14 Suppl 5:S14. doi: 10.1186/1471-2105-14-S5-S14. Epub 2013 Apr 10.
CLASS: constrained transcript assembly of RNA-seq reads.
Song L, Florea L.