convertimpute – Convert IMPUTE format to MultiPhen format

convertimpute

:: DESCRIPTION

convertimpute is a software for converting  IMPUTE format to format used by MultiPhen software

::DEVELOPER

Dr Lachlan J Coin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 convertimpute

:: MORE INFORMATION

Convert2Sbml / Convert2Matlab – Convert Metabolic Network Source files into SBML / MATLAB files

Convert2Sbml / Convert2Matlab

:: DESCRIPTION

Convert2Sbml / Convert2Matlab is the Java tool to convert various metabolic network source files into SBML / MATLAB files.

::DEVELOPER

CSB – Computational Systems Biology Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

Convert2Sbml / Convert2Matlab

:: MORE INFORMATION

PRIDE Converter 2.5.7 – Converts Mass Spectrometry Data into PRIDE XML

PRIDE Converter 2.5.7

:: DESCRIPTION

PRIDE Converter 2 converts mass spectrometry data from most common data formats into valid PRIDE XML for submission to the publicly available PRIDE database. It presents a convenient, wizard-like graphical user interface, and includes efficient access to the Ontology Lookup Service.

::DEVELOPER

PRIDE Converter Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

PRIDE Converter

:: MORE INFORMATION

Citation

Barsnes et. al:
PRIDE Converter: making proteomics data-sharing easy
Nat Biotechnol. 2009 Jul;27(7):598-9.

Cote RG & Griss J, et al.,
The PRIDE Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium.
Mol Cell Proteomics. 2012 Sep 4.

Tbl2KnownGene – Convert NCBI.tbl to UCSC knownGene.txt data file

Tbl2KnownGene

:: DESCRIPTION

Tbl2KnownGene is a wrapper tool that parses the contents of a NCBI .tbl annotation table and produces a UCSC Known Genes annotation table.

::DEVELOPER

Computational Biology Lab at Indiana State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

Tbl2KnownGene

:: MORE INFORMATION

Citation

Bioinformation. 2014 Aug 30;10(8):544-7. doi: 10.6026/97320630010544. eCollection 2014.
Tbl2KnownGene: A command-line program to convert NCBI.tbl to UCSC knownGene.txt data file.
Bai Y

ConvertCufflinksToExcel – Convert Cufflinks Output Files into Microsoft Excel

ConvertCufflinksToExcel

:: DESCRIPTION

ConvertCufflinksToExcel is a program to convert Cufflinks output files into easily readable Microsoft Excel tables using Apache’s POI library

::DEVELOPER

Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • JDK

:: DOWNLOAD

 ConvertCufflinksToExcel 

:: MORE INFORMATION

iConvert – Convert Genotype Allele Formats

iConvert

:: DESCRIPTION

The iConvert program allows to convert genotype allele formats (any format for any SNP chip contained in the SNPchiMp tool).

::DEVELOPER

iConvert team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  MacOsX / Linux
  • Python

:: DOWNLOAD

 iConvert

:: MORE INFORMATION

Citation

SNPchiMp v.3: integrating and standardizing single nucleotide polymorphism data for livestock species.
Nicolazzi EL, Caprera A, Nazzicari N, Cozzi P, Strozzi F, Lawley C, Pirani A, Soans C, Brew F, Jorjani H, Evans G, Simpson B, Tosser-Klopp G, Brauning R, Williams JL, Stella A.
BMC Genomics. 2015 Apr 10;16(1):283.

CrossMap 0.1.6 – Convert Genome Coordinates Between Assemblies

CrossMap 0.1.6

:: DESCRIPTION

CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies.

::DEVELOPER

CrossMap team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Python
  • C++ Compiler

:: DOWNLOAD

  CrossMap

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Apr 1;30(7):1006-7. doi: 10.1093/bioinformatics/btt730. Epub 2013 Dec 18.
CrossMap: a versatile tool for coordinate conversion between genome assemblies.
Zhao H1, Sun Z, Wang J, Huang H, Kocher JP, Wang L.

bioscripts.convert 0.4 – Biopython Scripts for Converting Molecular Sequences

bioscripts.convert 0.4

:: DESCRIPTION

bioscripts.convert provides scripts that use Biopython internally to simply convert multiple files on the commandline.

::DEVELOPER

Paul-Michael Agapow and Austin Burt (a.burt@imperial.ac.uk), Dept. Biology, University College London

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 bioscripts.convert

:: MORE INFORMATION

PyMsXML 0.5.4 – Convert Vendor Specific Mass Spectrometry file formats to open XML file formats

PyMsXML 0.5.4

:: DESCRIPTION

PyMsXML is a python script for converting vendor specific mass spectrometry data files for Applied Biosystems’ Q-Star, 4700, 4800, Mariner, and Voyager mass spectrometers from their raw binary form, to either of the emerging XML file formats for mass spectra: mzXML, from the Sashimi Glossolalia project of the Institute for Systems Biology (ISB); and mzData, from the Proteome Standardization Initiative (PSI) project of the Human Proteome Organization (HUPO).

::DEVELOPER

Edwards Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

 PyMsXML

:: MORE INFORMATION