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http://www.windowsazure.com/en-us/
An open and flexible cloud platform that enables you to quickly build, deploy and manage applications across a global network of Microsoft-managed datacenters.
Proper citation: Windows Azure (RRID:SCR_011880) Copy
https://basespace.illumina.com/home/sequence
Cloud platform to be directly integrated in to the industry?s leading sequencing platforms, with no cumbersome and time consuming data transfer steps.
Proper citation: BaseSpace (RRID:SCR_011881) Copy
https://sites.google.com/site/biovlab/
Cloud Computing and a graphical workflow composer that uses distributed computing resources on demand.''''
Proper citation: BioVLAB (RRID:SCR_011882) Copy
Offers genome analysis resources for cloud computing platforms such as Amazon EC2.
Proper citation: CloudBioLinux (RRID:SCR_011883) Copy
http://weizhong-lab.ucsd.edu/rammcap/cgi-bin/rammcap.cgi
Metagenomic software pipeline for analysis and comparison of very large metagenomes with fast clustering and functional annotation.
Proper citation: RAMMCAP (RRID:SCR_011927) Copy
http://euler.bc.edu/marthlab/scotty/scotty.php/
A tool to assist in the designing of RNA Seq experiments that have adequate power to detect differential expression at the level required to achieve experimental aims.
Proper citation: Scotty (RRID:SCR_011889) Copy
http://www.cs.ucr.edu/~jianxing/IsoInfer.html
A C/C++ program to infer isoforms based on short RNA-Seq (single-end and paired-end) reads, exon-intron boundary and TSS/PAS information.
Proper citation: IsoInfer (RRID:SCR_011892) Copy
http://bioinformatics.childhealthresearch.org.au/software/fusionfinder/
A perl-based software package, which can be used to find fusion transcript candidates in RNA-Seq data.
Proper citation: FusionFinder (RRID:SCR_011894) Copy
A desktop application for the bench biologists to analyse RNA-Seq and microarray expression data. It performs gene-centric analyses such as differential expression and pathways using well-established R modules, integrates data from multiple sources, and enables editing of R commands., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Guide (RRID:SCR_011903) Copy
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
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
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
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
https://code.google.com/p/rseqflow/
An RNA-Seq analysis pipeline which offers an express implementation of analysis steps for RNA sequencing datasets.
Proper citation: RseqFlow (RRID:SCR_011909) Copy
https://code.google.com/p/seqpipe/
A command line-based pipeline framework for bioinformatics research.
Proper citation: SeqPipe (RRID:SCR_011862) Copy
http://1001genomes.org/software/shore.html
A mapping and analysis pipeline for short read data produced on the Illumina platform.
Proper citation: SHORE (RRID:SCR_011863) Copy
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
http://sourceforge.net/projects/mirplant/
A user-friendly plant miRNA prediction tool.
Proper citation: miRPlant (RRID:SCR_012105) Copy
http://pypedal.sourceforge.net/
A pedigree analysis software package that provides tools for error checking, mathematical analysis, report generation, pedigree simulation, and data visualization.
Proper citation: PyPedal (RRID:SCR_012104) Copy
http://sourceforge.net/projects/simulatepcr/
Software that can be run from the command line for high throughput applications which can calculate all products from large lists of primers and probes compared to a large sequence database such as nt.
Proper citation: Simulate PCR (RRID:SCR_012106) Copy
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