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http://bayescall.sourceforge.net/
An efficient model-based base-calling algorithm for high-throughput sequencing.
Proper citation: naiveBayesCall (RRID:SCR_011866) Copy
http://pages.cs.wisc.edu/~bsettles/abner/
A software tool for molecular biology text analysis. At ABNER''s core is a statistical machine learning system using linear-chain conditional random fields (CRFs) with a variety of orthographic and contextual features.
Proper citation: ABNER (RRID:SCR_011868) Copy
http://transcriptome.ens.fr/eoulsan/
A versatile framework based on the Hadoop implementation of the MapReduce algorithm, dedicated to high throughput sequencing data analysis on distributed computers.
Proper citation: Eoulsan (RRID:SCR_011901) Copy
A literature search tool providing gene and signal transduction pathway mining within NCBI''''s PubMed database. Its sophisticated gene recognition and intuitive color coding increase the readability of abstracts and lets you analyze signal transduction pathways, diseases and tissue associations in a snap. Note: LitInspector has become part of the Literature & Pathways module of the Genomatix Software Suite.
Proper citation: LitInspector (RRID:SCR_011870) Copy
An open-source program for doing molecular docking.
Proper citation: AutoDock Vina (RRID:SCR_011958) Copy
http://cran.r-project.org/web/packages/vegan/index.html
Ordination methods, diversity analysis and other functions for community and vegetation ecologists.
Proper citation: vegan (RRID:SCR_011950) Copy
http://scalpel.sourceforge.net/
A software package for detecting INDELs (INsertions and DELetions) mutations in a reference genome which has been sequenced with next-generation sequencing technology (e.g., Illumina).
Proper citation: Scalpel (RRID:SCR_012107) Copy
http://sourceforge.net/projects/mtoolbox/
Software for a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data.
Proper citation: MToolBox (RRID:SCR_012112) Copy
http://sourceforge.net/projects/snpratiotest/
Software to calculate the number of significant SNPs in pathway divided by the number of SNPs in pathway.
Proper citation: SNP ratio test (RRID:SCR_012070) Copy
https://code.google.com/p/compomics-utilities/
A software library containing code shared by many research projects, amongst others containing panels for visualizing spectra and chromatograms and objects for representing peptides and proteins etc. This library can be of use to other research groups doing computational proteomics.
Proper citation: compomics-utilities (RRID:SCR_012073) Copy
http://sourceforge.net/projects/viewmol/
Software providing a graphical front end for computational chemistry programs.
Proper citation: Viewmol (RRID:SCR_012088) Copy
http://qutemol.sourceforge.net/
Open source (GPL) software providing an interactive, high quality molecular visualization system.
Proper citation: QuteMol (RRID:SCR_012089) Copy
https://code.google.com/p/pride-converter-2/
Suite of software tools that allows users to convert search result files into PRIDE XML, generate mzTab skeleton files that can be used as a basis to submit quantitative and gel-based MS data, and post-process PRIDE XML files by filtering out contaminants and empty spectra.
Proper citation: PRIDE Converter 2 (RRID:SCR_012051) Copy
http://sourceforge.net/projects/open-ms/
An algorithm to align LC-MS samples and to match corresponding ion species across samples.
Proper citation: OpenMS (RRID:SCR_012042) Copy
http://obi-warp.sourceforge.net/
Software that aligns matrices along a single axis using Dynamic Time Warping (DTW) and a one-to-one (bijective) interpolated warp function.
Proper citation: OBI-Warp (RRID:SCR_012041) Copy
http://sourceforge.net/projects/icplquant/
A proteomics software tool for quantitatively analyzing large mass spectrometric datasets acquired from ICPL based proteomics experiments.
Proper citation: ICPL ESIQuant (RRID:SCR_012047) Copy
http://www.bioconductor.org/packages/2.11/bioc/html/easyRNASeq.html
Software that calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as ''RPKM'' or by the ''DESeq'' or ''edgeR'' package.
Proper citation: easyRNASeq (RRID:SCR_012020) Copy
https://code.google.com/p/allim/
A user-friendly software tool to estimate allele-specific gene expression.
Proper citation: Allim (RRID:SCR_012114) Copy
http://sourceforge.net/projects/nailsystemsbiology/
A set of software tools to simplify the range of computational activities involved in regulatory network inference. It is technology-independent and includes an interface layer to allow easy integration of components into other applications. It is implemented in MATLAB and is available for all researchers to use.
Proper citation: NAIL (RRID:SCR_012134) Copy
https://code.google.com/p/localali/
A fast and scalable local network alignment software tool for the identification of functionally conserved modules in multiple networks. LocalAli outperforms all existing algorithms in terms of coverage, consistency and scalability, meanwhile retains a high precision in the identification of functionally coherent subnetworks.
Proper citation: LocalAli (RRID:SCR_012147) Copy
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