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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
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
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
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
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
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
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
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
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
An alignment, junction calling, and feature quantification pipeline specifically designed for Illumina RNA-Seq data.
Proper citation: RUM (RRID:SCR_008818) Copy
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
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
http://cran.r-project.org/web/packages/svd/
Interfaces to various state-of-art SVD and eigensolvers.
Proper citation: svd (RRID:SCR_008805) Copy
Merging Two Gene Expression Studies via Cross Platform Normalization.
Proper citation: XPN (RRID:SCR_008845) Copy
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
http://roadmapepigenomics.org/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 11, 2022. Project for human epigenomic data from experimental pipelines built around next-generation sequencing technologies to map DNA methylation, histone modifications, chromatin accessibility and small RNA transcripts in stem cells and primary ex vivo tissues selected to represent normal counterparts of tissues and organ systems frequently involved in human disease. Consortium expects to deliver collection of normal epigenomes that will provide framework or reference for comparison and integration within broad array of future studies. Consortium is also committed to development, standardization and dissemination of protocols, reagents and analytical tools to enable research community to utilize, integrate and expand upon this body of data.
Proper citation: Roadmap Epigenomics Project (RRID:SCR_008924) Copy
A compression utility designed to be a replacement for compress.
Proper citation: Gzip (RRID:SCR_009291) Copy
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
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
http://metagenomics.atc.tcs.com/compression/DELIMINATE/
A practical implementation of a novel compression approach that can rapidly compress FASTA files containing genomic sequence data in a loss-less fashion.
Proper citation: DELIMINATE (RRID:SCR_008956) Copy
Web-based tool that allows users to view comparisons of genetic and physical maps. The package also includes tools for curating map data. (entry from Genetic Analysis Software)
Proper citation: CMAP (RRID:SCR_009034) Copy
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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