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http://www.bios.unc.edu/research/genomic_software/BBSeq/

A Powerful and Flexible Approach to the Analysis of RNA Sequence Count Data.

Proper citation: BBSeq (RRID:SCR_011877) Copy   

•   Source: SciCrunch Registry

http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/

Software for an iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth.

Proper citation: IDBA-UD (RRID:SCR_011912) Copy   

•   Source: SciCrunch Registry

http://www.unav.es/genetica/oncofuse.html

Software tool designed to predict the oncogenic potential of fusion genes found by Next-Generation Sequencing in cancer cells.

Proper citation: Oncofuse (RRID:SCR_011904) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.mdanderson.org/main/PRADA:Overview

A pipeline to analyze paired end RNA-Seq data to generate gene expression values (RPKM) and gene-fusion candidates.

Proper citation: PRADA (RRID:SCR_011906) Copy   

•   Source: SciCrunch Registry

https://mcdonaldlab.biology.gatech.edu/r-sap/

An automated bioinformatics pipeline that analyzes and quantitates high-throughput RNA-Seq datasets.

Proper citation: R-SAP (RRID:SCR_011907) Copy   

•   Source: SciCrunch Registry

http://mapman.gabipd.org/web/guest/robin

Software package for RNA-Seq-based transcriptomics. Used to analyse Illumina/Solexa-based RNA-Seq data, Affymetrix data and generic tabular two color or single channel array data. Offers variety of quality control methods that can be used to gain overview of experimental data technical quality and structure.

Proper citation: RobiNA (RRID:SCR_011908) Copy   

•   Source: SciCrunch Registry

http://www.optimaldesign.com/ArrayMiner/ArrayMiner.htm

A set of analysis tools using advanced algorithms to reveal the true structure of your gene expression data.

Proper citation: ArrayMiner (RRID:SCR_011955) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/mirplant/

A user-friendly plant miRNA prediction tool.

Proper citation: miRPlant (RRID:SCR_012105) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/slidesort-bpr/

Software using a reference-free method for detecting clusters of breakpoints from the chromosomal rearrangements.

Proper citation: SlideSort-BPR (RRID:SCR_012079) Copy   

•   Source: SciCrunch Registry

http://www.bioinf.jku.at/software/fabia/fabia.html

A model-based technique for biclustering that is clustering rows and columns simultaneously.

Proper citation: FABIA (RRID:SCR_012002) Copy   

•   Source: SciCrunch Registry

http://mfpaq.sourceforge.net/

Software that allows fast and user-friendly verification of Mascot result files, as well as data quantification using isotopic labeling methods (SILAC/ICAT) or label free approaches (spectral counting, MS signal comparison).

Proper citation: MFPaQ (RRID:SCR_012049) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/multiplierz/

An open-source Python-based environment that provides a scriptable framework for efficient access to manufacturers'' proprietary data files via mzAPI.

Proper citation: multiplierz (RRID:SCR_012058) Copy   

•   Source: SciCrunch Registry

http://www.computationalbioenergy.org/meta-storms.html

Optimized GPU-based software to efficiently measure the quantitative phylogenetic similarity among massive amount of microbial community samples.

Proper citation: GPU-Meta-Storms (RRID:SCR_012029) Copy   

•   Source: SciCrunch Registry

http://opencobra.sourceforge.net/openCOBRA/Welcome.html

Software Python package that provides support for basic COnstraint-Based Reconstruction and Analysis (COBRA) methods.

Proper citation: COBRApy (RRID:SCR_012096) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/netcoffee/

A fast and accurate algorithm which allows to find a global alignment of multiple protein-protein interaction networks.

Proper citation: NetCoffee (RRID:SCR_012095) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.fccc.edu/software/OpenSource/FGDP/FGDP.shtml

A Java-based, Microarray or Genechip data analysis system.

Proper citation: FGDP (RRID:SCR_008910) Copy   

•   Source: SciCrunch Registry

http://www.labmedmolge.unisa.it/inglese/research/imir

A modular pipeline for comprehensive analysis of smallRNA-Seq data, comprising specific tools for adapter trimming, quality filtering, DE analysis, target prediction by integrating multiple open source modules and resources in an automated workflow.

Proper citation: iMir (RRID:SCR_009496) Copy   

•   Source: SciCrunch Registry

http://www.stanford.edu/group/wonglab/SpliceMap/

A de novo splice junction discovery and alignment tool.

Proper citation: SpliceMap (RRID:SCR_009650) Copy   

•   Source: SciCrunch Registry

http://dna.engr.uconn.edu/?page_id=105

Software package that can be used to infer isoform and gene expression levels from high-throughput transcriptome sequencing (RNA-Seq) data.

Proper citation: IsoEM (RRID:SCR_009993) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/bitseq/

A software application for inferring expression levels of individual transcripts from sequencing (RNA-Seq) data and estimating differential expression (DE) between conditions.

Proper citation: BitSeq (RRID:SCR_009904) Copy   

•   Source: SciCrunch Registry