Searching the RRID Resource Information Network
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.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GreenPhylDB Resource Report Resource Website 10+ mentions |
GreenPhylDB (RRID:SCR_002834) | GreenPhylDB | data or information resource, production service resource, analysis service resource, database, service resource, data analysis service | A database designed for plant comparative and functional genomics based on complete genomes. It comprises complete proteome sequences from the major phylum of plant evolution. The clustering of these proteomes was performed to define a consistent and extensive set of homeomorphic plant families. Based on this, lists of gene families such as plant or species specific families and several tools are provided to facilitate comparative genomics within plant genomes. The analyses follow two main steps: gene family clustering and phylogenomic analysis of the generated families. Once a group of sequences (cluster) is validated, phylogenetic analyses are performed to predict homolog relationships such as orthologs and ultraparalogs. | comparative genomics, genome, functional genomics, genomics, gene family, homolog, bio.tools |
uses: Gene Ontology is listed by: bio.tools is listed by: Debian has parent organization: CIRAD |
PMID:20864446 | Free, Freely available, Available for download | biotools:greenphyldb, nif-0000-02928 | http://greenphyl.cirad.fr http://www.greenphyl.org/v3/ https://bio.tools/greenphyldb |
SCR_002834 | 2026-02-17 09:59:59 | 19 | ||||||
|
ANDES Resource Report Resource Website 10+ mentions |
ANDES (RRID:SCR_002791) | software application, data processing software, data analysis software, software resource, software toolkit | Software library and a suite of applications, written in Perl and R, for deep sequencing statistical analyses. | deep sequencing, biomarker detection, statistical analysis, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20633290 | Free, Freely available, Available for download | biotools:andes, OMICS_01119 | https://bio.tools/andes | SCR_002791 | Statistical tools for the Analyses of Deep Sequencing (ANDES), Statistical tools for the Analyses of Deep Sequencing, Statistical tools for the ANalyses of Deep Sequencing | 2026-02-17 10:00:03 | 25 | ||||||
|
NCBI database of Genotypes and Phenotypes (dbGap) Resource Report Resource Website 500+ mentions |
NCBI database of Genotypes and Phenotypes (dbGap) (RRID:SCR_002709) | dbGaP | storage service resource, data or information resource, database, service resource, data repository | Database developed to archive and distribute clinical data and results from studies that have investigated interaction of genotype and phenotype in humans. Database to archive and distribute results of studies including genome-wide association studies, medical sequencing, molecular diagnostic assays, and association between genotype and non-clinical traits. | clinical, trial, genotype, interaction, homology, cell, morphology, interaction, phenotype, molecular diagnosis, genetic recombination, gold standard, bio.tools |
is used by: International Genomics of Alzheimers Project is used by: NIDDK Inflammatory Bowel Disease Genetics Consortium is used by: NIH Heal Project is used by: Genomic Data Commons Data Portal (GDC Data Portal) is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is listed by: re3data.org is listed by: NIDDK Information Network (dkNET) is listed by: bio.tools is listed by: Debian is related to: NIDDK Central Repository is related to: eMERGE Network: electronic Medical Records and Genomics is related to: Framingham Heart Study is related to: PhenoExplorer is related to: Chronic Renal Insufficiency Cohort Study is related to: DbGaP Cleaner is related to: Psychiatric Genomics Consortium is related to: ISCA Consortium is related to: Allen Institute for Brain Science has parent organization: NCBI is parent organization of: Resource for Genetic Epidemiology Research on Adult Health and Aging |
NLM | PMID:24297256 PMID:17898773 |
Restricted | nif-0000-23342, OMICS_00263, biotools:dbgap, r3d100010788 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=gap https://bio.tools/dbgap https://doi.org/10.17616/R3GS4K |
SCR_002709 | database of Genotypes and Phenotypes (dbGaP), dbGaP, NCBI, Database of Genotypes and Phenotypes | 2026-02-17 10:00:01 | 683 | ||||
|
discoSnp Resource Report Resource Website 1+ mentions |
discoSnp (RRID:SCR_002612) | software application, data processing software, data analysis software, software resource, sequence analysis software | Software designed for discovering Single Nucleotide Polymorphism (SNP) from raw sets of reads obtained with Next Generation Sequencers (NGS). | single nucleotide polymorphism, snp discovery, discover snp, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
SOFIPROTEOL under the FASO project PEAPOL ; INRIA ANR-12-BS02-0008 |
PMID:25404127 | Free, Freely available | biotools:discosnp, OMICS_00267 | https://bio.tools/discosnp https://sources.debian.org/src/discosnp/ |
SCR_002612 | DiscoSnp++, discovering Single Nucleotide Polymorphism, discovering Single Nucleotide Polymorphism (discoSNP) | 2026-02-17 09:59:49 | 9 | |||||
|
SuperPred: Drug classification and target prediction Resource Report Resource Website |
SuperPred: Drug classification and target prediction (RRID:SCR_002691) | SuperPred | data access protocol, data or information resource, database, web service, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 24,2025. Publicly available web-server to predict medical indication areas based on properties and similarity of chemical compounds. The web-server translates a user-defined molecule into a structural fingerprint that is compared to about 6300 drugs, which are enriched by 7300 links to molecular targets of the drugs, derived through text mining followed by manual curation. Links to the affected pathways are provided. The similarity to the medical compounds is expressed by the Tanimoto coefficient that gives the structural similarity of two compounds. A similarity score higher than 0.85 results in correct ATC prediction for 81% of all cases. As the biological effect is well predictable, if the structural similarity is sufficient, the web-server allows prognoses about the medical indication area of novel compounds and to find new leads for known targets. The combination of physicochemical property and similarity searching provides the possibility to detect new biologically active compounds and novel targets for drug-like compounds. SuperPred can be applied for drug repositioning purposes, too. A further intention of SuperPred is to find side effects elicited by drugs caused through off-target hits. | drug, drug class, drug target, addiction, anatomical therapeutic chemical, application area, biological activity, chemical, chemical classification, chemical property, classification, compound, molecular target, molecule, nervous system, pathway, pharmacological property, physicochemical property, prediction, activity spectra, substance, structural similarity, structure, tanimoto coefficient, tanimoto score, target prediction, target-prediction server, therapeutic approach, therapeutic property, drug classification, target prediction, similarity score, target, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany |
SFB 449 ; IRTG Berlin-Boston-Kyoto and Deutsche Krebshilfe. ; DFG |
PMID:18499712 PMID:24878925 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:superpred, nif-0000-00415 | https://bio.tools/superpred | SCR_002691 | 2026-02-17 10:00:02 | 0 | |||||
|
Rainbow Resource Report Resource Website 10+ mentions |
Rainbow (RRID:SCR_002724) | software application, data processing software, data analysis software, software resource, sequence analysis software | Software developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. | software, tool, clustering, assembling, short, read, restriction, site, DNA, sequence, analysis, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:22942077 DOI:10.1093/bioinformatics/bts482 |
Free, Freely available, Available for download | SCR_015992, OMICS_03722, biotools:rainbow | https://bio.tools/rainbow https://sources.debian.org/src/bio-rainbow/ |
SCR_002724 | RAD-seq: Restriction-site Associated DNA sequencing, Bio-rainbow, RAD-seq | 2026-02-17 10:00:02 | 41 | ||||||
|
Coding Potential Calculator Resource Report Resource Website 100+ mentions |
Coding Potential Calculator (RRID:SCR_002764) | CPC | production service resource, analysis service resource, service resource, software resource, data analysis service | A Support Vector Machine-based classifier to assesses the protein-coding potential of a transcript based on six biologically meaningful sequence features. CPC can discriminate coding from noncoding transcripts with high accuracy and speed. In addition to predicting the coding potential of the input transcripts, the CPC web server also graphically displays detailed sequence features and additional annotations of the transcript that may facilitate users' further investigation. The coding potential calculator tool reads FASTA data format as input. | fasta, transcript, protein coding, coding potential, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Peking University; Beijing; China |
PMID:17631615 | Free, Freely available | biotools:cpc, rid_000106 | https://bio.tools/cpc | SCR_002764 | 2026-02-17 09:59:58 | 198 | ||||||
|
Human Disease Ontology Resource Report Resource Website 1+ mentions |
Human Disease Ontology (RRID:SCR_000476) | DO | data or information resource, ontology, database, controlled vocabulary | Comprehensive hierarchical controlled vocabulary for human disease representation.Open source ontology for integration of biomedical data associated with human disease. Disease Ontology database represents comprehensive knowledge base of inherited, developmental and acquired human diseases. | obo, pathological, organismal, cellular, disease, biomedical, health, neurologic disease, neurological disorder, phenotype, bio.tools, |
is used by: DOAF is listed by: BioPortal is listed by: OBO is listed by: bio.tools is listed by: Debian is related to: PharmGKB Ontology is related to: GWASdb is related to: NUgene Project is related to: FunDO is related to: Neurocarta has parent organization: University of Maryland School of Medicine; Maryland; USA |
NHGRI U24 HG012557 | PMID:22080554 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-35926, nlx_157432, SCR_003491, biotools:disease_ontology | http://disease-ontology.org/ https://bio.tools/disease_ontology http://purl.obolibrary.org/obo/doid.obo |
http://do-wiki.nubic.northwestern.edu/index.php/Main_Page | SCR_000476 | Human Disease Ontology Knowledgebase, Disease Ontology | 2026-02-17 09:59:27 | 5 | |||
|
AETIONOMY Resource Report Resource Website 1+ mentions |
AETIONOMY (RRID:SCR_000232) | AETIONOMY | data or information resource, portal, organization portal, consortium | Consortium founded to establish mechanism-based taxonomies for Alzheimer's and Parkinson's disease and other neurodegenerative disorders (NDD), with the goal of facilitating development of more effective and targeted treatments. To do this, the consortium collects and analyzes data to: * Create new ways to combine underutilized data currently available in the literature, public databases, and from private companies * Determine how to dynamically organize and structure different types of knowledge about NDD * Determine how to apply this knowledge to construct new patient group classification * Identify correlations between disease features at molecular, tissue or organ-specific, and clinical levels * Identify sub-groups of patients based on the molecular cause of their disease, as opposed to the nature and location of their symptoms * Deliver data, tools, and recommendations for the biomedical community in the treatment of NDD A mechanism-based taxonomy is hoped to advance the: # Description and organization of the indication-specific data # Linking of data to disease models, based on causal and correlative relationships The expected outcome of AETIONOMY is a new NDD taxonomy system that distinguishes mixed pathologies, allowing for new features or classes to be added into the taxonomy, all with the goal of aiding drug and biomarker discovery. | drug development, drug, taxonomy, biomarker, etiology, epidemiology, neuroimaging, mechanism, clinical, clinical trial, database, classification, biological pathway, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Fraunhofer Institute for Algorithms and Scientific Computing SCAI; North Rhine-Westphalia; Germany |
IMI ; EFPIA |
nlx_157972, biotools:AETIONOMY | https://bio.tools/AETIONOMY | SCR_000232 | 2026-02-17 09:59:25 | 3 | |||||||
|
RSEM Resource Report Resource Website 50+ mentions |
RSEM (RRID:SCR_000262) | data analysis software, software application, data processing software, software resource | Software package for quantifying gene and isoform abundances from single end or paired end RNA Seq data. Accurate transcript quantification from RNA Seq data with or without reference genome. Used for accurate quantification of gene and isoform expression from RNA-Seq data. | quantifying, gene, isoform, abundance, single, end, paired, RNA seq, data, transcript, reference, genome, bio.tools |
is listed by: OMICtools is listed by: GitHub is listed by: bio.tools is listed by: Debian has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
PMID:21816040 | Free, Available for download, Freely available | OMICS_01966, OMICS_01287, biotools:rsem, SCR_013027 | https://github.com/deweylab/RSEM https://github.com/deweylab/RSEM/releases https://bio.tools/rsem https://sources.debian.org/src/rsem/ |
SCR_000262 | RSEM, RNA-Seq by Expectation-Maximization, RSEM-v1.3.0 | 2026-02-17 09:59:25 | 94 | ||||||
|
DESeq Resource Report Resource Website 100+ mentions |
DESeq (RRID:SCR_000154) | DESeq | data analysis software, software application, data processing software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Software for differential gene expression analysis based on the negative binomial distribution. It estimates variance-mean dependence in count data from high-throughput sequencing assays and tests for differential expression. | gene expression, binomial, differential, negative binomial distribution, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is hosted by: Bioconductor |
PMID:20979621 DOI:10.1186/s13059-014-0550-8 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01306, biotools:deseq | https://bio.tools/deseq https://sources.debian.org/src/r-bioc-deseq2/ |
SCR_000154 | 2026-02-17 09:59:24 | 473 | ||||||
|
POPBAM Resource Report Resource Website |
POPBAM (RRID:SCR_000464) | POPBAM | data analysis software, software application, data processing software, software resource | A tool to perform evolutionary or population-based analyses of next-generation sequencing data. POPBAM takes a BAM file as its input and can compute many widely used evolutionary genetics measures in sliding windows across a genome. | next-generation sequencing, evolution, population, bam, genome, evolutionary genetics, c++, short read, sequence alignment, sliding window, command-line, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: University of Rochester; New York; USA |
PMID:24027417 | Free, Available for download, Freely available | biotools:popbam, OMICS_01559 | https://bio.tools/popbam | http://popbam.sourceforge.net/ | SCR_000464 | 2026-02-17 09:59:27 | 0 | |||||
|
GASV Resource Report Resource Website 1+ mentions |
GASV (RRID:SCR_000061) | GASV | data analysis software, software application, data processing software, software resource | Software tool for identifying structural variants (SVs) from paired-end sequencing data.GASV distribution includes three components that are typically run in succession: the BAM file of unique paired-read mappings is processed; structural variants are identified by clustering discordant fragments; and a probabilistic algorithm improves the specificity of GASV predictions. | paired-end sequencing data, structural variant, probabilistic algorithm, discordant fragment, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: GASVPro has parent organization: Brown University; Rhode Island; USA |
Burroughs Wellcome Fund ; Department of Defense Breast Cancer Research ; ADVANCE Program at Brown University ; NSF 0548311 |
PMID:19477992 | Free, Available for download, Freely available | biotools:gasv, OMICS_01352 | http://compbio.cs.brown.edu/projects/gasv/ https://bio.tools/gasv |
SCR_000061 | Geometric Analysis of Structural Variants | 2026-02-17 09:59:23 | 4 | ||||
|
BAIT Resource Report Resource Website 1+ mentions |
BAIT (RRID:SCR_000511) | BAIT | software application, data processing software, data analysis software, software resource, data visualization software | Software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data. | create strand inheritance plots, strand-seq, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24028793 | Free, Available for download, Freely available | biotools:bait, OMICS_01531 | https://bio.tools/bait | SCR_000511 | BAIT - Software to help analyse Strand-Seq data | 2026-02-17 09:59:28 | 1 | |||||
|
MPscan Resource Report Resource Website |
MPscan (RRID:SCR_000587) | MPscan | data access protocol, web service, software resource | Web tool for index free mapping of multiple short reads on a genome. | linux, macos, next-generation sequencing, genome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: ATGC: Montpellier bioinformatics platform |
Free, Available for download, Freely available | biotools:mpscan, OMICS_00670 | https://bio.tools/mpscan | SCR_000587 | MPscan: index free mapping of multiple short reads on a genome | 2026-02-17 09:59:28 | 0 | ||||||
|
SplitSeek Resource Report Resource Website 1+ mentions |
SplitSeek (RRID:SCR_001012) | software application, data processing software, data analysis software, software resource, sequence analysis software | THIS RESOURCE IS NO LONGER IN SERVICE, documented September 20, 2016. A program for de novo prediction of splice junctions in RNA-seq data. | bioinformatics alignment, sequence analysis software, de novo, prediction, rna seq, rna, splice junction, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:20236510 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:splitseek, OMICS_01253 | https://bio.tools/splitseek | http://www.uppmax.uu.se/software/splitseek | SCR_001012 | 2026-02-17 09:59:33 | 1 | ||||||
|
Skylign Resource Report Resource Website 10+ mentions |
Skylign (RRID:SCR_001176) | Skylign | production service resource, analysis service resource, service resource, software resource, data analysis service | A tool for creating logos representing both sequence alignments and profile hidden Markov models. The interactive logos enable scrolling, zooming, and inspection of underlying values. Skylign can avoid sampling bias in sequence alignments by down-weighting redundant sequences and by combining observed counts with informed priors. It also simplifies the representation of gap parameters, and can optionally scale letter heights based on alternate calculations of the conservation of a position. | sequence alignment, profile, logo, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Janelia Research |
PMID:24410852 | Creative Commons Attribution License, v3 Unported | biotools:skylign, OMICS_02182 | https://bio.tools/skylign | SCR_001176 | Skylign - Interactive logos for alignments and profile HMMs | 2026-02-17 09:59:36 | 13 | |||||
|
sim4cc Resource Report Resource Website |
sim4cc (RRID:SCR_001204) | software application, data processing software, software resource, image analysis software, alignment software | Software tool as cross species spliced alignment program.Heuristic sequence alignment tool for comparing cDNA sequence with genomic sequence containing homolog of gene in another species. | Cross species spliced alignment, unix, sequence alignment, cdna sequence, genomic sequence, homolog, gene, splice, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Johns Hopkins University; Maryland; USA |
NSF CLS20163A; Sloan Research Fellowship ; NLM R01 LM006845 |
PMID:19429899 | Free, Available for download, Freely available | biotools:sim4cc, OMICS_02145 | https://bio.tools/sim4cc | SCR_001204 | 2026-02-17 09:59:35 | 0 | ||||||
|
bsseq Resource Report Resource Website 1+ mentions |
bsseq (RRID:SCR_001072) | software application, data processing software, data analysis software, software resource, sequence analysis software | R package with tools for analyzing and visualizing bisulfite sequencing data. | bisulfite sequencing, analyze, r, sequence analysis software, data analysis software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_01847, biotools:bsseq | https://bio.tools/bsseq | SCR_001072 | bsseq - Analyze manage and store bisulfite sequencing data | 2026-02-17 09:59:34 | 8 | |||||||
|
AutoAssemblyD Resource Report Resource Website |
AutoAssemblyD (RRID:SCR_001087) | software application, data processing software, data analysis software, software resource, sequence analysis software | Software which performs local and remote genome assembly by several assemblers based on an XML Template which can replace the large command lines required by most assemblers. | genome, genome assembly, xml, sequence analysis software, local genome assembly, remote genome assembly, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24143057 | Free, Available for download, Freely available | biotools:autoassemblyd, OMICS_00874 | https://bio.tools/autoassemblyd | SCR_001087 | 2026-02-17 09:59:35 | 0 |
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