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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.
A Galaxy framework-based online pipeline for reliable analysis of data generated by three types of CLIP-seq protocols: HITS-CLIP, PAR-CLIP and iCLIP. It provides both data processing and statistical analysis to determine candidate cross-linking regions, which are comparable to those regions identified from the original studies or using existing computational tools., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: PIPE-CLIP (RRID:SCR_005820) Copy
http://mint.bio.uniroma2.it/virusmint/
A virus protein interactions database that collects and annotates all the interactions between human and viral proteins and integrates this information in the human protein interaction network. It uses the PSI-MI standard and is fully integrated with the MINT database. You can search for any viral or human protein by entering either common names or database identifiers or display a complete viral interactome.
Proper citation: VirusMINT (RRID:SCR_005987) Copy
http://omicsomics.blogspot.fr/
A computational biologist''s personal views on new technologies & publications on genomics & proteomics and their impact on drug discovery.
Proper citation: OMICS! OMICS! (RRID:SCR_008533) Copy
Service that allows you to process CEL files from Affymetrix, Inc. GeneChip Exon 1.0 ST Arrays to identify alternative splicing.
Proper citation: Exon Array Analyzer (RRID:SCR_008684) Copy
We share commentaries, news and announcement that advance our goal of helping clinical labs to adopt next generation sequencing for the analysis of diagnostic gene targets.
Proper citation: Omixon blog (RRID:SCR_010020) Copy
http://mcg.ustc.edu.cn/sdap1/cpss/index.html
Computational Platform for analysis of Small RNA deep Sequencing data BioStaCs group., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: CPSS (RRID:SCR_009395) Copy
http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index
Manually curated database of experimentally supported animal microRNA targets. Collection of experimentally supported miRNA gene interactions.
Proper citation: TarBase (RRID:SCR_010841) Copy
A website which assigns molecular functional effects of non-synonymous SNPs based on structure and sequence analysis.
Proper citation: SNPs3D (RRID:SCR_010787) Copy
http://tools.genxpro.net/omiras/
A web server for the annotation, comparison and visualization of interaction networks of non-coding RNAs derived from small RNA-Sequencing experiments of two different conditions.
Proper citation: omiRas (RRID:SCR_010833) Copy
http://compbio.med.harvard.edu/CGHweb/
Data analysis service enabling users to analyse their array-CGH data with multiple algorithms simultaneously.
Proper citation: CGHweb (RRID:SCR_010923) Copy
http://agvgd.iarc.fr/index.php
A freely available, web-based program that combines the biophysical characteristics of amino acids and protein multiple sequence alignments to predict where missense substitutions in genes of interest fall in a spectrum from enriched delterious to enriched neutral.
Proper citation: Align-GVGD (RRID:SCR_010772) Copy
http://cosmoss.org/bm/plantapdb
A phylogeny-based comprehensive database of plant transcription associated proteins.
Proper citation: PlanTAPDB (RRID:SCR_010897) Copy
http://www.mutationtaster.org/
Evaluates disease-causing potential of sequence alterations.
Proper citation: MutationTaster (RRID:SCR_010777) Copy
http://hyperbrowser.uio.no/hb/
A generic web-based system, providing statistical methodology and computing power to handle a variety of biological inquires on genomic datasets.
Proper citation: Genomic HyperBrowser (RRID:SCR_010909) Copy
https://genome-cancer.ucsc.edu/
A suite of web-based tools to visualize, integrate and analyze cancer genomics and its associated clinical data. It is possible to display your own clinical data within one of their datasets.
Proper citation: UCSC Cancer Genomics Browser (RRID:SCR_011796) Copy
http://www.ebi.ac.uk/Tools/sss/wublast/
Tool to find regions of sequence similarity within selected protein databases quickly, with minimum loss of sensitivity.
Proper citation: WU-BLAST (RRID:SCR_011824) Copy
http://data-analysis.charite.de/care/
Comprehensive database of cancer relevant proteins and compound interactions supported by experimental knowledge.Knowledgebase for drug-target relationships related to cancer as well as for supporting information or experimental data.
Proper citation: CancerResource (RRID:SCR_011945) Copy
This blog will appeal to those dealing with the practical day to day work of biological data analysis and presentation.
Proper citation: Blue Collar Bioinformatics (RRID:SCR_012913) Copy
http://www.benoslab.pitt.edu/comir/
Data analysis service that predicts whether a given mRNA is targeted by a set of miRNAs. ComiR uses miRNA expression to improve and combine multiple miRNA targets for each of the four prediction algorithms: miRanda, PITA, TargetScan and mirSVR. The composite scores of the four algorithms are then combined using a support vector machine trained on Drosophila Ago1 IP data.
Proper citation: ComiR (RRID:SCR_013023) Copy
A web-server for fast comparative functional profiling of metagenomes.
Proper citation: CoMet (RRID:SCR_011925) Copy
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