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http://www.bioconductor.org/packages/2.12/bioc/html/charm.html

Software package that implements analysis tools for DNA methylation data generated using Nimblegen microarrays and the McrBC protocol.

Proper citation: charm (RRID:SCR_012992) Copy   

•   Source: SciCrunch Registry

http://rnaseq-mats.sourceforge.net/

Software tool to detect differential alternative splicing events from RNA-Seq data. Calculates P value and false discovery rate that difference in isoform ratio of gene between two conditions exceeds given user defined threshold. Can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. Handles replicate RNA-Seq data from both paired and unpaired study design.

Proper citation: Multivariate Analysis of Transcript Splicing (RRID:SCR_013049) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/BiSeq.html

Software package that provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data.

Proper citation: BiSeq (RRID:SCR_012993) Copy   

•   Source: SciCrunch Registry

http://trinityrnaseq.sourceforge.net/

Software for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.

Proper citation: Trinity (RRID:SCR_013048) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/MEDME.html

Software that allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments.

Proper citation: MEDME (RRID:SCR_012995) Copy   

•   Source: SciCrunch Registry

https://github.com/brentp/methylcode

A single program that takes of bisulfite-treated reads and outputs per-base methylation data.

Proper citation: MethylCoder (RRID:SCR_012997) Copy   

•   Source: SciCrunch Registry

http://grassius.org/

A public resource composed of a collection of databases, computational and experimental resources that relate to the control of gene expression in the grasses, and their relationship with agronomic traits. As knowledge on the interactions of transcription factors (TFs) and cis-regulatory elements in the promoters of the genes that they regulate continues to accumulate, the information is acquired by GRASSIUS, either through contributions by the community, or by literature analysis. The overarching objective of GRASSIUS is to provide a one-stop resource that will facilitate research and communication within the plant community with regards to genome-wide regulation of gene expression processes.

Proper citation: GRASSIUS (RRID:SCR_012999) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/lofreq/

A fast and sensitive variant-caller for inferring single-nucleotide variants (SNVs) from high-throughput sequencing data.

Proper citation: LoFreq (RRID:SCR_013054) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/genecounter/

A computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression of eukaryotes, prokaryotes, as well as organisms with no available genome reference sequence.

Proper citation: GENE-counter (RRID:SCR_013056) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/snptools/

A suite of software tools that enables integrative SNP analysis in next generation sequencing data with large cohorts.

Proper citation: SNPTools (RRID:SCR_013052) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/swiftng/

An open source package for primary data analysis on next-gen sequence data from images to basecalls. Currently Swift is targeted toward Solexa/Illumina sequencing, but is designed to be platform agnostic.

Proper citation: Swift (RRID:SCR_013018) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/cloudaligner/

A map/reduce based application for mapping short reads generated by the next-generation sequencing machines.

Proper citation: CloudAligner (RRID:SCR_012962) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/Rolexa.html

Software that provides probabilistic base calling, quality checks and diagnostic plots for Solexa sequencing data.

Proper citation: Rolexa (RRID:SCR_013017) Copy   

•   Source: SciCrunch Registry

http://www.ra.cs.uni-tuebingen.de/software/InCroMAP/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5,2023. Integrated analysis of cross-platform microarray and pathway data.

Proper citation: InCroMAP (RRID:SCR_012964) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/tracetuner/

Software tool for base and quality calling of trace files from DNA sequencing instruments.

Proper citation: TraceTuner (RRID:SCR_013019) Copy   

•   Source: SciCrunch Registry

http://genomeview.org/

A next-generation stand-alone genome browser and editor initiated in the BSB group at VIB and currently developed at Broad Institute.

Proper citation: GenomeView (RRID:SCR_012968) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/seqminer/

Software for a genome wide mapping data interpretation platform for NGS (ChIPSeq).

Proper citation: seqMINER (RRID:SCR_013020) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/mireap/

A software tool which can be used to identify both known and novel microRNAs from small RNA libraries deeply sequenced by Solexa/454/Solid technology.

Proper citation: MIREAP (RRID:SCR_013025) Copy   

•   Source: SciCrunch Registry

http://www.lgm.upmc.fr/mirena/index.html

A software tool to find microRNAs with high accuracy and no learning at genome scale and from deep sequencing data.

Proper citation: MIReNA (RRID:SCR_013024) Copy   

•   Source: SciCrunch Registry

https://mig.molbiol.ox.ac.uk/mig/

Allows the user to conveniently compare data from many loci., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MIG (RRID:SCR_012972) Copy   

•   Source: SciCrunch Registry