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http://www.reddit.com/r/bioinformatics/
A subreddit dedicated to bioinformatics, computational genomics and systems biology.
Proper citation: reddit (RRID:SCR_011983) Copy
http://www.genboree.org/java-bin/EpigenomeAtlas/workbench.jsp?isPublic=yes&context=EpigenomeAtlas
Service where users are able to upload and store data, access bioinformatics tools, and perform analyses.
Proper citation: Genboree Workbench (RRID:SCR_011864) Copy
https://bioinf.eva.mpg.de/ibis/
An accurate, fast and easy-to-use base caller for the Illumina sequencing system, which significantly reduces the error rate and increases the output of usable reads.
Proper citation: Ibis (RRID:SCR_011865) Copy
http://bayescall.sourceforge.net/
An efficient model-based base-calling algorithm for high-throughput sequencing.
Proper citation: naiveBayesCall (RRID:SCR_011866) Copy
http://www-huber.embl.de/users/anders/HTSeq/doc/count.html
Script distributed with the HT-Seq Python framework for processing RNA-seq or DNA-seq data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: htseq-count (RRID:SCR_011867) Copy
http://bioinfo.au.tsinghua.edu.cn/software/RNAseqViewer/
Software to visualize the various data from the RNA-Seq analyzing process, for single or multiple samples.
Proper citation: RNAseqViewer (RRID:SCR_011900) 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 user-Frendly RNA-Seq gene eXpression analysis tool, empowered by the concept of cloud-computing.
Proper citation: FX (RRID:SCR_011902) Copy
http://www.eecs.ucf.edu/~xiaoman/SIOMICS/SIOMICS.html
A software to de novo identify motifs in large sequence datasets such as those from ChIP-seq experiments.
Proper citation: SIOMICS (RRID:SCR_011990) 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
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://www.cs.helsinki.fi/u/lmsalmel/coral/
An error correction algorithm for correcting reads from DNA sequencing platforms such as the Illumina Genome Analyzer or HiSeq platforms or Roche/454 Genome Sequencer.
Proper citation: Coral (RRID:SCR_011849) Copy
http://www.dei.unipd.it/~sambofra/abacus.html
An Algorithm based on a BivAriate CUmulative Statistic to identify SNPs significantly associated with a disease within predefined sets of SNPs such as pathways or genomic regions.
Proper citation: ABACUS (RRID:SCR_013039) Copy
http://sourceforge.net/projects/oncosts/
Software for a web-based Laboratory Information Management System for sample and analysis tracking in oncogenomic experiments.
Proper citation: Onco-STS (RRID:SCR_012990) Copy
http://www.bioconductor.org/packages/2.12/bioc/html/RankProd.html
Software using a non-parametric method for identifying differentially expressed (up- or down- regulated) genes based on the estimated percentage of false predictions (pfp).
Proper citation: RankProd (RRID:SCR_013046) Copy
http://sourceforge.net/projects/nxgview/
A virtual software pipeline that contains several PERL modules for processing next generation sequencing data.
Proper citation: NxGview (RRID:SCR_012994) Copy
http://sourceforge.net/projects/bamformatics/
Software that provides a coherent and consistent approach to analysis of high-throughput sequencing data.
Proper citation: Bamformatics (RRID:SCR_013041) Copy
http://www.bioconductor.org/packages/2.12/bioc/html/MEDIPS.html
Software developed for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq).
Proper citation: MEDIPS (RRID:SCR_012996) Copy
http://sourceforge.net/projects/bsmapper/
Sequence mapper for bisulfite sequencing reads for DNA methylation studies.
Proper citation: BSmapper (RRID:SCR_012998) Copy
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