mzMatch/PeakML 2.0 – Metabolomics Data Analysis

mzMatch/PeakML 2.0

:: DESCRIPTION

mzMatch is a modular, open source and platform independent data processing pipeline for metabolomics LC/MS data written in the Java language. It was designed to provide small tools for the common processing tasks for LC/MS data. The mzMatch environment was based entirely on the PeakML file format and core library, which provides a common framework for all the tools.

::DEVELOPER

mzMatch team

:: SCREENSHOTS

mzMatch

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java/ R

:: DOWNLOAD

 mzMatch/PeakML

:: MORE INFORMATION

Citation

PeakML/mzMatch: a file format, Java library, R library, and tool-chain for mass spectrometry data analysis.
Scheltema RA, Jankevics A, Jansen RC, Swertz MA, Breitling R.
Anal Chem. 2011 Apr 1;83(7):2786-93. doi: 10.1021/ac2000994

Sipros 3.0 – Proteomics Data Analysis software

Sipros 3.0

:: DESCRIPTION

Sipros is a database-searching algorithm for peptide and protein identification in shotgun proteomics.

:: DESCRIPTION

the Pan lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Python
  • R package

:: DOWNLOAD

 Sipros

:: MORE INFORMATION

Citation

Sipros/ProRata: a versatile informatics system for quantitative community proteomics.
Wang Y, Ahn TH, Li Z, Pan C.
Bioinformatics. 2013 Aug 15;29(16):2064-5. doi: 10.1093/bioinformatics/btt329.

ProtViz 0.6.8 – Proteomics Data Analysis & Visualization

ProtViz 0.6.8

:: DESCRIPTION

protViz is an R package that helps with quality checks, vizualizations and analysis of mass spectrometry data, coming from proteomics experiments. The package is developed, tested and used at the Functional Genomics Center Zurich. We use this package mainly for prototyping, teaching, and having fun with proteomics data. But it can also be used to do solid data analysis for small scale data sets.

::DEVELOPER

The Functional Genomics Center Zurich (FGCZ)

:: SCREENSHOTS

n/a

::REQUIREMENTS

  • Linux / Solaris / MacOS X
  • R package

:: DOWNLOAD

 ProtViz

:: MORE INFORMATION

SimGlycan 5.94 – Glycan & Glycopeptide MS/MS Data Analysis Tool

SimGlycan 5.94

:: DESCRIPTION

SimGlycan® predicts the structure of glycans and glycopeptides using mass spectrometry data. SimGlycan® accepts the experimental MS/MS data generated by a mass spectrometer, matches them with its own database of theoretical fragments and generates a list of probable candidate structures.

::DEVELOPER

PREMIER Biosoft

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

SimGlycan Demo

:: MORE INFORMATION

Order SimGlycan

KegArray 1.2.4 – Microarray Data Analysis & Cluster

KegArray 1.2.4

:: DESCRIPTION

KegArray is a Java application that provides an environment for analyzing both transcriptome data (gene expression profiles) and metabolome data (compound profiles). Tightly integrated with the KEGG database, KegArray enables you to easily map those data to KEGG resources including PATHWAY, BRITE and genome maps.

::DEVELOPER

Kanehisa Laboratories

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

KegArray

:: MORE INFORMATION

Citation

Methods Mol Biol. 2012;802:19-39.
The KEGG databases and tools facilitating omics analysis: latest developments involving human diseases and pharmaceuticals.
Kotera M, Hirakawa M, Tokimatsu T, Goto S, Kanehisa M.

ProteoWizard 3.0.21193 – Proteomics Data Analysis

ProteoWizard 3.0.21193

:: DESCRIPTION

ProteoWizard is a modular and extensible set of open-source, cross-platform tools and software libraries for proteomics data analysis.The libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard chemistry and LCMS dataset computations.

::DEVELOPER

ProteoWizard Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX

:: DOWNLOAD

ProteoWizard

:: MORE INFORMATION

Citation

Kessner D, Chambers M, Burke R, Agus D, Mallick P.
ProteoWizard: open source software for rapid proteomics tools development.
Bioinformatics. 2008 Nov 1;24(21):2534-6. Epub 2008 Jul 7.

ARB 6.0.6 – Sequence Database Handling and data analysis

ARB 6.0.6

:: DESCRIPTION

The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked to the respective sequence entries is structured according to phylogeny or other user defined criteria.

::DEVELOPER

Prof. Dr. Wolfgang Liebl

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 ARB

:: MORE INFORMATION

Citation:

Wolfgang Ludwig, et al.
ARB: a software environment for sequence data.
Nucleic Acids Research. 2004. 32(4):1363-1371.

Perseus v1.6.15.0 – Shotgun Proteomics Data Analysis

Perseus v1.6.15.0

:: DESCRIPTION

Perseus is a software package for shotgun proteomics data analysis, which helps researchers to extract biologically meaningful information from their MaxQuant output such as posttranslational modifications.

::DEVELOPER

Jürgen Cox

:: SCREENSHOTS

Perseus

:: REQUIREMENTS

  • Windows 64bit
  • .NET Framework 4.5

:: DOWNLOAD

 Perseus

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012;13 Suppl 16:S12. doi: 10.1186/1471-2105-13-S16-S12. Epub 2012 Nov 5.
1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data.
Cox J, Mann M.

CisGenome 2.0 – ChIP-chip and ChIP-seq Data Analysis

CisGenome 2.0

:: DESCRIPTION

CisGenome is a software system for analyzing genome-wide chromatin immunoprecipitation (ChIP) data. CisGenome is designed to meet all basic needs of ChIP data analyses, including visualization, data normalization, peak detection, false discovery rate computation, gene-peak association, and sequence and motif analysis. In addition to implementing previously published ChIP–microarray (ChIP-chip) analysis methods, the software contains statistical methods designed specifically for ChlP sequencing (ChIP-seq) data obtained by coupling ChIP with massively parallel sequencing. The modular design of CisGenome enables it to support interactive analyses through a graphic user interface as well as customized batch-mode computation for advanced data mining. A built-in browser allows visualization of array images, signals, gene structure, conservation, and DNA sequence and motif information.

::DEVELOPER

Ji Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux

:: DOWNLOAD

CisGenome

:: MORE INFORMATION

Citation

Hongkai Ji, Hui Jiang, Wenxiu Ma, David S. Johnson, Richard M. Myers and Wing H.Wong (2008)
An integrated software system for analyzing ChIP-chip and ChIP-seq data.
Nature Biotechnology, 26: 1293-1300. doi:10.1038/nbt.1505

RseqFlow 2.2 – RNA-seq Data Analysis Workflow

RseqFlow 2.2

:: DESCRIPTION

RseqFlow is a workflow which can implement a set of RNA-Seq analysis, such as performing quality control (QC) for sequencing data, generating signal tracks of mapped reads, calculating expression levels, and identifying differentially expressed genes. The workflow allows users to express multi-step RNA-Seq analysis by just providing sequencing RNA-Seq datasets and typing a few commands in an easy-to-use environment.

::DEVELOPER

Ting Chen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows / MacOsX
  • Virtual Machine

:: DOWNLOAD

 RseqFlow

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Sep 15;27(18):2598-600. Epub 2011 Jul 27.
RseqFlow: workflows for RNA-Seq data analysis.
Wang Y, Mehta G, Mayani R, Lu J, Souaiaia T, Chen Y, Clark A, Yoon HJ, Wan L, Evgrafov OV, Knowles JA, Deelman E, Chen T.