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http://sourceforge.net/projects/tumorhats/
A software tool that calls the amplified alleles, and thus amplified haplotype, in copy number aberration regions in next generation sequencing tumor data.
Proper citation: HATS (RRID:SCR_013044) Copy
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
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
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
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
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
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
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
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
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
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
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
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
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
http://sourceforge.net/projects/seqminer/
Software for a genome wide mapping data interpretation platform for NGS (ChIPSeq).
Proper citation: seqMINER (RRID:SCR_013020) Copy
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
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
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
http://sourceforge.net/projects/msa-edna/
Software for Multiple Sequence Alignment for Transcription Factor Binding Sites using Di nucleotides dependencies and relying on Free Interaction energies between neighbouring DNA bases to stabilise substitution energy of the alignment.
Proper citation: EDNA (RRID:SCR_012981) Copy
http://bioconductor.org/packages/2.12/bioc/html/cn.mops.html
A data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data.
Proper citation: cn.mops (RRID:SCR_013036) Copy
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