BLISS 0.7 – Identify Batch Effects in RNA Expression Data

BLISS 0.7

:: DESCRIPTION

BLISS (The Batch anaLysIS Suite) is intended to help identify batch effects in RNA expression data.  It has been tested on miRNA and mRNA results derived from the illumina sequencing platform.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 BLISS

:: MORE INFORMATION

eRNA 1.01 – RNA Data Analysis Tool

eRNA 1.01

:: DESCRIPTION

eRNA is an RNA data analysis tool for high-throughput RNA sequencing experiments

::DEVELOPER

eRNA team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux
  • Perl
  • R

:: DOWNLOAD

 eRNA 

:: MORE INFORMATION

Citation:

BMC Genomics. 2014 Mar 5;15:176. doi: 10.1186/1471-2164-15-176.
eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing.
Yuan T, Huang X, Dittmar RL, Du M, Kohli M, Boardman L, Thibodeau SN, Wang L

BioAnalyzer 2100 – Analysis of BioAnalyzer data

BioAnalyzer 2100

:: DESCRIPTION

The Agilent 2100 BioAnalyzer is a nanofluidics device that preforms size fractionation and quantification of small samples of DNA, RNA, or Protein. In addition, the BioAnalyzer is able to preform flow cytometry on small numbers of cells.

::DEVELOPER

the MIT BioMicro Center

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 BioAnalyzer

:: MORE INFORMATION

mseq 1.2 – Modeling non-uniformity in Short-read Rates in RNA-Seq data

mseq 1.2

:: DESCRIPTION

mseq is an R package for modeling non-uniformity in short-read rates in RNA-Seq data.

::DEVELOPER

Jun Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX/  Linux / WIndows
  • R Package

:: DOWNLOAD

 mseq

:: MORE INFORMATION

Citation

Jun Li, Hui Jiang, and Wing H Wong (2010)
Modeling non-uniformity in short-read rates in RNA-Seq data.
Genome Biology 11(5): R50.

ChromA 0.9 – Alignment for Chromatography Mass Spectrometry Data

ChromA 0.9

:: DESCRIPTION

ChromA (Chromatogram Alignment) provides the Dynamic Time Warping algorithm for the alignment of data from the domain of Gas- and Liquid-Chromatography Mass-Spectrometry. It uses additional constraints and can be configured to use different local functions to evaluate the similarity of mass spectra between chromatograms. It allows the definition of anchors, which are the positions of conserved compounds, constraining the alignment and providing a speedup. Furthermore, ChromA provides different visualizations of the alignment, as well as a textual format for further processing of chromatograms.

::DEVELOPER

Nils Hoffmann

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac / Windows
  • Java

:: DOWNLOAD

ChromA

:: MORE INFORMATION

Citation

ChromA: Signal Based Retention Time Alignment for Chromatography-Mass Spectrometry Data
Nils Hoffmann; Jens Stoye
Bioinformatics 2009; doi: 10.1093/bioinformatics/btp343

VRMLGen 1.4.6 – An R Package for 3D Data Visualization on the Web

VRMLGen 1.4.6

:: DESCRIPTION

VRMLGen is a free R software package to generate 3D representations of biological data in the Virtual Reality Markup Language

::DEVELOPER

VRMLGen team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

VRMLGen

:: MORE INFORMATION

Citation

Enrico Glaab, Jonathan M. Garibaldi, Natalio Krasnogor
vrmlgen: An R Package for 3D Data Visualization on the Web
Journal of Statistical Software, 2010 DOI: 10.18637/jss.v036.i08

apLCMS 6.6.6 – adaptive processing of high resolution LC/MS data

apLCMS 6.6.6

:: DESCRIPTION

apLCMS is an R package which designed for the processing of LC/MS based metabolomics data. It starts with a group of LC/MS files in the same folder, and generates a table with features in the rows and intensities in the columns.

::DEVELOPER

Tianwei Yu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R

:: DOWNLOAD

apLCMS

:: MORE INFORMATION

Citation

apLCMS–adaptive processing of high-resolution LC/MS data.
Yu T, Park Y, Johnson JM, Jones DP.
Bioinformatics. 2009 Aug 1;25(15):1930-6. doi: 10.1093/bioinformatics/btp291.

rapmad – Robust Analysis of Peptide MicroArray Data

rapmad

:: DESCRIPTION

rapmad is an R-package for the Robust Analysis of Peptide MicroArray Data. It is an automated, multi-step approach that combines several computational and statistical procedures to improve the quality of peptide microarray data and thus enable a more reliable analysis.

::DEVELOPER

The Institute for Translational Oncology and Immunology (TrOn)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux /MacOsX
  • R package

:: DOWNLOAD

   rapmad

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Aug 4;12:324. doi: 10.1186/1471-2105-12-324.
rapmad: Robust analysis of peptide microarray data.
Renard BY, Löwer M, Kühne Y, Reimer U, Rothermel A, Türeci O, Castle JC, Sahin U.

SHORE 0.9.3 – Analysis Suite for Illumina Short Read Data

SHORE 0.9.3

:: DESCRIPTION

SHORE is a mapping and analysis pipeline for short DNA sequences produced on Illumina Genome Analyzer and Hiseq 2000, Life Technology SOLiD, 454 Genome Sequencer FLX and PacBio RS platforms. It is designed for projects whose analysis strategy involves mapping of reads to a reference sequence. This reference sequence does not necessarily have to be from the same species, since weighted and gapped alignments allow for accuracy even in diverged regions. SHORE provides various prediction algorithms for genomic polymorphisms, i.e. SNPs, structural variants (indels, CNVs, unsequenced regions), SNPs and SV prediction in heterozygous or pooled samples, as well as peak detection for ChIP-Seq analysis and quantitative analysis of mRNA-Seq and sRNA-Seq.

::DEVELOPER

Dept. Weigel

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SHORE

:: MORE INFORMATION

Citation

Genome Res. 2008 Dec;18(12):2024-33. Epub 2008 Sep 25.
Sequencing of natural strains of Arabidopsis thaliana with short reads.
Ossowski S, Schneeberger K, Clark RM, Lanz C, Warthmann N, Weigel D.

SNPTools 1.0 – SNP analysis in Next Generation Sequencing data

SNPTools 1.0

:: DESCRIPTION

SNPTools is a suite of tools that enables integrative SNP analysis in next generation sequencing data with large cohorts. It not only calls SNP in a population with high sensitivity and accuracy, but also employs a novel imputation engine to achieve highly accurate genotype calls in an efficient way.

::DEVELOPER

Human Genome Sequencing Center, Baylor College of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler

:: DOWNLOAD

 SNPTools

:: MORE INFORMATION

Citation

Genome Res. 2013 Jan 7. [Epub ahead of print]
An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data.
Wang Y, Lu J, Yu J, Gibbs RA, Yu F.