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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://deconseq.sourceforge.net/

Software tool to automatically detect and efficiently remove sequence contaminations from genomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface. The user can upload FASTA or FASTQ files and select the databases used for contamination screening, including seven human genomes, bacterial genomes, and viral genomes. The user can set the thresholds interactivly and see the results directly using the functionality of the graphical interface. The results can be downloaded in joined or separated files in different formats. The coverage-identity plots provide additional information that can guide the selections of the thresholds using color coded points and connecting lines.

Proper citation: DeconSeq (RRID:SCR_007006) Copy   

•   Source: SciCrunch Registry

http://bioinfo-out.curie.fr/projects/vamp/

Software for visualization and Analysis of CGH arrays, transcriptome and other Molecular Profiles.

Proper citation: VAMP (RRID:SCR_008527) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.6/bioc/html/DEGseq.html

R package to identify differentially expressed genes from RNA-Seq data.

Proper citation: DEGseq (RRID:SCR_008480) Copy   

•   Source: SciCrunch Registry

http://emboss.sourceforge.net/

Software analysis package for molecular biology community. Automatically copes with data in variety of formats and allows transparent retrieval of sequence data from web. Libraries are provided with package. Provides toolkit for creating bioinformatics applications or workflows. Provides set of sequence analysis programs. Provided programs cover areas such as sequence alignment, rapid database searching with sequence patterns, protein motif identification, nucleotide sequence pattern analysis, codon usage analysis for small genomes, rapid identification of sequence patterns in large scale sequence sets, and presentation tools for publication.

Proper citation: EMBOSS (RRID:SCR_008493) Copy   

•   Source: SciCrunch Registry

http://www.who.int/en/

The directing and coordinating authority responsible for public health within the United Nations system. The WHO Regional Office for Europe (WHO/Europe) is one of the six regional offices around the world. It serves the WHO European Region, which comprises 53 countries from the Atlantic to the Pacific oceans. WHO/Europe collaborates with a range of public health stakeholders in the Region and globally, to ensure that coordinated action is taken to develop and implement efficient health policies and to strengthen health systems. WHO/Europe is made up of public health, scientific, and technical experts.

Proper citation: World Health Organization (RRID:SCR_008505) Copy   

•   Source: SciCrunch Registry

http://lowelab.ucsc.edu/tRNAscan-SE

Web server to search for tRNA genes in genomic sequence. If you would like to run tRNAscan-SE locally, you can get the UNIX source code (gzip''d tar file).

Proper citation: tRNAscan-SE (RRID:SCR_008637) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/drivermutationidentification/

Computational tool developed to help identify cancer-associated ''driver'' mutations from ''passenger'' ones in a cancer genome.

Proper citation: DMI (RRID:SCR_008599) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://www.ingenuity.com/products/pathways_analysis.html

A web-based software application that enables users to analyze, integrate, and understand data derived from gene expression, microRNA, and SNP microarrays, metabolomics, proteomics, and RNA-Seq experiments, and small-scale experiments that generate gene and chemical lists. Users can search for targeted information on genes, proteins, chemicals, and drugs, and build interactive models of experimental systems. IPA allows exploration of molecular, chemical, gene, protein and miRNA interactions, creation of custom molecular pathways, and the ability to view and modify metabolic, signaling, and toxicological canonical pathways. In addition to the networks and pathways that can be created, IPA can provide multiple layering of additional information, such as drugs, disease genes, expression data, cellular functions and processes, or a researchers own genes or chemicals of interest.

Proper citation: Ingenuity Pathway Analysis (RRID:SCR_008653) Copy   

•   Source: SciCrunch Registry

http://www.tutegenomics.com/

A robust, secure, medical-grade, web application that lives in the cloud and has the ability to analyze and annotate entire human genomes in a rapid and cost-effective way.

Proper citation: Tute Genomics (RRID:SCR_008672) Copy   

•   Source: SciCrunch Registry

http://homes.esat.kuleuven.be/~bioiuser/eXtasy/

A pipeline for ranking nonsynonymous single nucleotide variants given a specific phenotype.

Proper citation: eXtasy (RRID:SCR_008671) Copy   

•   Source: SciCrunch Registry

http://bg.upf.edu/condel/home

A method to assess the outcome of nonsynonymous SNVs using a consensus deleteriousness score that combines various tools (e.g. SIFT, Polyphen2, MutationAssessor).

Proper citation: Condel (RRID:SCR_008584) 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