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http://bioconductor.org/packages/2.12/bioc/html/seqbias.html

Software package that implements a model of per-position sequencing bias in high-throughput sequencing data using a simple Bayesian network, the structure and parameters of which are trained on a set of aligned reads and a reference genome sequence.

Proper citation: seqbias (RRID:SCR_006832) Copy   

•   Source: SciCrunch Registry

http://weizhong-lab.ucsd.edu/cd-hit-otu/

Data analysis service and software program that perform Operantional Taxonomic Units (OTUs) finding. It uses a three-step clustering for identifying OTUs. The first-step clustering is raw read filtering and trimming. The second step is error-free reads picking.. At the last step, OTU clustering is done at different distanct cutoffs (0.01, 0.02, 0.03... 0.12).

Proper citation: CD-HIT-OTU (RRID:SCR_006983) Copy   

•   Source: SciCrunch Registry

http://www2.cancer.ucl.ac.uk/medicalgenomics/medusa/

A computational pipeline bringing together numerous software packages to perform a full analysis of MeDIP-seq data, including sequence alignment, quality control (QC), and determination and annotation of DMRs.

Proper citation: MeDUSA (RRID:SCR_006926) Copy   

•   Source: SciCrunch Registry

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

Comprehensive differentially methylated regions (DMR) analysis based on bimodal normal distribution model and weighted cost function for regional methylation analysis optimization.

Proper citation: eDMR (RRID:SCR_006960) Copy   

•   Source: SciCrunch Registry

http://202.97.205.78/epidiff/QDMRTutorial.jsp

Software that provides a quantitative approach to quantify methylation difference and identify DMRs from genome-wide methylation profiles by adapting Shannon entropy.

Proper citation: QDMR (RRID:SCR_007162) Copy   

•   Source: SciCrunch Registry

http://users.utu.fi/mijopi/Pripper/

A tool that can be used to predict caspase cleavage sites from human protein sequences.

Proper citation: Pripper (RRID:SCR_007129) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/evora/

R package for quantifying variation in DNA methylation as a cancer biomarker.

Proper citation: EVORA (RRID:SCR_007329) Copy   

•   Source: SciCrunch Registry

http://seurat.r-forge.r-project.org/

Software tool which provides interactive visualization capability for the integrated analysis of high-dimensional gene expression data. Visual analytics for the integrated analysis of microarray data.

Proper citation: SEURAT (RRID:SCR_007322) Copy   

•   Source: SciCrunch Registry

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

Bioinformatics analysis software tool for optimized ChIP-seq peak detection written in R.

Proper citation: peakrots (RRID:SCR_007453) Copy   

•   Source: SciCrunch Registry

https://github.com/steinmann/peakzilla

An algorithm to identify transcription factor binding sites from ChIP-seq data.

Proper citation: Peakzilla (RRID:SCR_007471) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/DWD/

This software package provides the implementation of distance weighted discrimination (DWD) using an interior point method for the solution of second order cone programming problems.

Proper citation: DWD (RRID:SCR_008760) Copy   

•   Source: SciCrunch Registry

http://cbil.upenn.edu/RUM/

An alignment, junction calling, and feature quantification pipeline specifically designed for Illumina RNA-Seq data.

Proper citation: RUM (RRID:SCR_008818) Copy   

•   Source: SciCrunch Registry

https://github.com/armintoepfer/QuasiRecomb/releases

A jumping hidden Markov model that describes the generation of the viral quasispecies and a method to infer its parameters by analysing next generation sequencing data.

Proper citation: QuasiRecomb (RRID:SCR_008812) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/isva/

An algorithm for feature selection in the presence of potential confounding factors.

Proper citation: isva (RRID:SCR_008772) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/svd/

Interfaces to various state-of-art SVD and eigensolvers.

Proper citation: svd (RRID:SCR_008805) Copy   

•   Source: SciCrunch Registry

https://genome.unc.edu/xpn/

Merging Two Gene Expression Studies via Cross Platform Normalization.

Proper citation: XPN (RRID:SCR_008845) Copy   

•   Source: SciCrunch Registry

http://tvap.genome.wustl.edu/tools/music/

A set of tools aimed at determining the significance of somatic mutations discovered within a given cohort of cancer samples, incorporating the cohort''s alignment data, variant lists and any relevant clinical data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MuSiC (RRID:SCR_008792) Copy   

•   Source: SciCrunch Registry

http://www.gzip.org/

A compression utility designed to be a replacement for compress.

Proper citation: Gzip (RRID:SCR_009291) Copy   

•   Source: SciCrunch Registry

http://bioinfo.au.tsinghua.edu.cn/software/seqsaw/

A package for mapping of spliced reads and unbiased detection of novel splice junctions from RNA-seq data.

Proper citation: SeqSaw (RRID:SCR_009185) Copy   

•   Source: SciCrunch Registry

http://www.medinfopoli.polimi.it/GAAS/

An integrated software framework for efficient management, analysis and visualization of large amounts of gene expression data across replicated experiments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GAAS (RRID:SCR_008967) Copy   

•   Source: SciCrunch Registry