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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
eProbalign Resource Report Resource Website |
eProbalign (RRID:SCR_013247) | analysis service resource, data analysis service, production service resource, service resource | Data analysis service that computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities. | multiple sequence alignments, partition function posterior probabilities, bio.tools |
uses: Probalign is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: New Jersey Institute of Technology; New Jersey; USA |
NIGMS R01 GM073082 | PMID:17485479 | OMICS_00975, biotools:eprobalign | https://bio.tools/eprobalign | SCR_013247 | eProbalign web server, EProbalign | 2026-08-07 09:27:50 | 0 | ||||||
|
CUPSAT Resource Report Resource Website 50+ mentions |
CUPSAT (RRID:SCR_010773) | CUPSAT | analysis service resource, data analysis service, production service resource, service resource | A tool to predict changes in protein stability upon point mutations. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:16845001 | biotools:cupsat, OMICS_00128 | https://bio.tools/cupsat | SCR_010773 | Cologne University Protein Stability Analysis Tool, CUPSAT: Cologne University Protein Stability Analysis Tool | 2026-08-07 09:27:23 | 86 | ||||||
|
LS-SNP/PDB Resource Report Resource Website 1+ mentions |
LS-SNP/PDB (RRID:SCR_010774) | LS-SNP/PDB | analysis service resource, data analysis service, production service resource, service resource | A web tool for genome-wide annotation of human SNPs. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Johns Hopkins University; Maryland; USA |
OMICS_00131, biotools:ls-snp | https://bio.tools/ls-snp | SCR_010774 | 2026-08-07 09:27:25 | 3 | ||||||||
|
PlantTFcat Resource Report Resource Website 10+ mentions |
PlantTFcat (RRID:SCR_010898) | PlantTFcat | analysis service resource, data analysis service, production service resource, service resource | A web-based analysis tool that is designed to identify and categorize plant TF/TR/CR genes from genome-scale protein and nucleic acid sequences by systematically analyzing InterProScan domain patterns in protein sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Samuel Roberts Noble Foundation |
PMID:24219505 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:planttfcat, OMICS_00559 | https://bio.tools/planttfcat | SCR_010898 | PlantTFcat: An Online Plant Transcription Factor and Transcriptional Regulator Categorization and Analysis Tool | 2026-08-07 09:27:21 | 46 | |||||
|
ArrayPipe Resource Report Resource Website 10+ mentions |
ArrayPipe (RRID:SCR_010934) | ArrayPipe | analysis service resource, data analysis service, production service resource, service resource | A flexible tool for visualizing and analyzing your two-colour microarray slides. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00744, biotools:arraypipe | https://bio.tools/arraypipe | SCR_010934 | 2026-08-07 09:27:26 | 15 | ||||||||
|
PREDDIMER Resource Report Resource Website 10+ mentions |
PREDDIMER (RRID:SCR_011963) | PREDDIMER | analysis service resource, data analysis service, production service resource, service resource | Prediction tool to reconstruct putative dimer conformations for given sequences of transmembrane protein fragments, which are considered as ideal alpha-helices. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24202542 | Free | OMICS_01614, biotools:preddimer | https://bio.tools/preddimer | SCR_011963 | PREDDIMER - Prediction tool for an ensemble of transmembrane ?-helical dimer conformations | 2026-08-07 09:27:34 | 15 | |||||
|
MethBase Resource Report Resource Website 1+ mentions |
MethBase (RRID:SCR_017487) | database, data or information resource, service resource | Central reference methylome database created from public BS-seq datasets. Provides methylation level at individual sites, regions of allele specific methylation, hypo- or hyper-methylated regions, partially methylated regions, and detailed meta data and summary statistics. | Methylome, database, public, BSseq, dataset, methylation, site, region, allele, specific, metadata, statistics, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Southern California; Los Angeles; USA |
Free, Freely available | BioTools:MethBase, biotools:Methbase | https://bio.tools/MethBase, https://bio.tools/MethBase, https://bio.tools/MethBase | SCR_017487 | MethBase: a reference methylome database | 2026-08-07 09:28:46 | 1 | |||||||
|
SnpSift Resource Report Resource Website 500+ mentions |
SnpSift (RRID:SCR_015624) | software resource, software toolkit, source code | Software toolkit for filtering and manipulating annotated files. After annotation, the software's filter function can find relevant genomic variants in large data files. | annotation, filtering, genomic variant, single nucleotide polymorphism, bio.tools |
is listed by: bio.tools is listed by: Debian works with: SnpEff |
PMID:22728672 | Open Source, Free, Available for download | biotools:snpsift | https://bio.tools/snpsift | SCR_015624 | SnpEff | 2026-08-07 09:28:23 | 631 | ||||||
|
Examl Resource Report Resource Website 50+ mentions |
Examl (RRID:SCR_016087) | Examl | software resource, software application, source code | Source code for large-scale phylogenetic analyses on whole-transcriptome and whole-genome alignments using supercomputers. | phylogenetic, analysis, database, large scale, whole genome, whole transcriptome, alignment, efficiency, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
Heidelberg Institute for Theoretical Studies | PMID:25819675 | Free, Available for download | OMICS_08024, biotools:ExaML | https://bio.tools/ExaML, https://sources.debian.org/src/examl/ | SCR_016087 | Examl:Exascale Maximum Likelihood | 2026-08-07 09:28:28 | 62 | ||||
|
PhenoFam Resource Report Resource Website |
PhenoFam (RRID:SCR_000640) | PhenoFam | software resource, software application | A web-based application that performs gene set enrichment analysis (GSEA) by employing structural and functional information on families of protein domains as annotation terms. | java, javascript, gene, gene set enrichment analysis, structure, function, protein domain, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20478033 | Free, Available for download, Freely available | OMICS_02230, biotools:phenofam | https://bio.tools/phenofam | SCR_000640 | 2026-08-07 09:25:03 | 0 | ||||||
|
VeryFastTree Resource Report Resource Website 1+ mentions |
VeryFastTree (RRID:SCR_023594) | software resource, software application, source code | Software tool for speeding up estimation of phylogenetic trees for large alignments through parallelization and vectorization strategies. | large alignments, phylogenetic tree, phylogenetic tree creation, bio.tools |
is listed by: bio.tools is related to: FastTree |
MICINN ; Xunta de Galicia ; ERDF |
PMID:32573652 DOI:10.1093/bioinformatics/btaa582 |
Free, Available for download, Freely available | biotools:veryfasttree | https://bio.tools/veryfasttree | SCR_023594 | 2026-08-07 09:29:57 | 8 | ||||||
|
ReadqPCR Resource Report Resource Website |
ReadqPCR (RRID:SCR_000030) | standalone software, software resource, software application | A software package that provides functions to read raw RT-qPCR data of different platforms. | standalone software, mac os x, unix/linux, windows, r, data import, gene expression, microtitre plate assay, qpcr, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor has parent organization: University College London; London; United Kingdom |
PMID:22748112 | Free, Available for download, Freely available | biotools:readqpcr, OMICS_03936 | https://bio.tools/readqpcr | SCR_000030 | ReadqPCR - Read qPCR data | 2026-08-07 09:24:55 | 0 | ||||||
|
mzMatch Resource Report Resource Website 1+ mentions |
mzMatch (RRID:SCR_000543) | software resource, software toolkit | A software to provide small tools for common processing tasks for LC/MS data. It is an extension to the metabolomics analysis pipeline mzMatch.R. The software is modular, open source, platform independent and written in Java. | metabolomics, analysis, java, tool, peak extraction, filtering, normalization, derivative detection, identification, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23162054 | Free, Available for download, Freely available, | biotools:mzmatch, OMICS_02642 | https://bio.tools/mzmatch | SCR_000543 | 2026-08-07 09:25:02 | 5 | |||||||
|
FLOSS Resource Report Resource Website |
FLOSS (RRID:SCR_000836) | FLOSS | software resource, software application | Software application that performs ordered subset analysis using MERLIN's ouput .lod file created with the --perFamily option. Ordered subset analysis uses covariate information to identify a more homogenous subset of families for linkage analysis. The homogeneous subset of families does not need to be specified a priori, and the covariates can include environmental exposures, quantitative traits, or linkage scores at another locus in the genome. The evidence for linkage is evaluated with a permutation test. (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:floss, nlx_154319 | https://bio.tools/floss | SCR_000836 | FLexible Ordered SubSet analysis | 2026-08-07 09:25:05 | 0 | |||||||
|
DINDEL Resource Report Resource Website 10+ mentions |
DINDEL (RRID:SCR_001827) | Dindel | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 7,2024. Software program for calling small indels from short-read sequence data ("next generation sequence data"). It is currently designed to handle only Illumina data. Dindel takes BAM files with mapped Illumina read data and enables researchers to detect small indels and produce a VCF file of all the variant calls. It has been written in C++ and can be used on Linux-based and Mac computers (it has not been tested on Windows operating systems). | indel, short-read, next generation sequence, illumina, gene, genetic, genomic, c++, linux, macos, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:20980555 DOI:10.1101/gr.112326.110 |
THIS RESOURCE IS NO LONGER IN SERVICE | , nlx_154283, OMICS_00096, biotools:dindel | https://bio.tools/dindel, https://sources.debian.org/src/dindel/ | http://www.sanger.ac.uk/resources/software/dindel/ | SCR_001827 | Dindel: Accurate indel calls from short-read data | 2026-08-07 09:25:18 | 44 | ||||
|
metabnorm Resource Report Resource Website |
metabnorm (RRID:SCR_001266) | standalone software, software resource, software application | Software tool as mixed model normalization method for metabolomics data.Uses normalization approach based on mixed model, with simultaneous estimation of correlation matrix. | Metabolomics datasets, corelation, normalization, identifying metabolites, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
Cancer Research UK Cambridge Institute ; Erik and Edith Fernström foundation ; Cancer Research UK |
PMID:24711654 | Free, Available for download, Freely available | OMICS_03548, biotools:metabnorm | https://bio.tools/metabnorm | SCR_001266 | 2026-08-07 09:25:11 | 0 | ||||||
|
PEDIGRAPH Resource Report Resource Website 10+ mentions |
PEDIGRAPH (RRID:SCR_001938) | Pedigraph | software resource, software application | A pedigree visualization program specifically designed to draw large, complex pedigrees. (entry from Genetic Analysis Software) Options include: * Full pedigree * Summarization * Extraction of individual pedigrees * Inbreeding calculation * Coancestry coefficient calculation * Color control * Drawing size * Page size and margins * Drawing styles | gene, genetic, genomic, c, c++, ms-windows, linux, pedigree, java, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
PMID:14986440 | Acknowledgement required, Copyrighted | biotools:pedigraph, OMICS_00212, nlx_154519 | https://bio.tools/pedigraph | SCR_001938 | 2026-08-07 09:25:20 | 17 | ||||||
|
Apollo Resource Report Resource Website 100+ mentions |
Apollo (RRID:SCR_001936) | Apollo | software resource, software application | A standalone Java application with a GUI (graphical user interface) for editing genome annotations. Like GBrowse, it allows users to scroll and zoom in on areas of interest in a sequence; authorized users can edit annotations and write the changes back to the underlying database. Apollo can run off GFF3 or a Chado database, and it can also integrate with remote services, such as BLAST and Primer BLAST analyses. | java, genome annotation, genome, annotation, windows, mac os x, linux, solaris, unix, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Generic Model Organism Database Project |
PMID:19439563 PMID:12537571 DOI:10.1186/gb-2002-3-12-research0082 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_11761, biotools:apollo, OMICS_01933 | https://bio.tools/apollo, https://sources.debian.org/src/aragorn/ | SCR_001936 | 2026-08-07 09:25:19 | 301 | ||||||
|
lsa_slurm Resource Report Resource Website 1+ mentions |
lsa_slurm (RRID:SCR_018134) | software resource, source code | Software tool to implement pre-assembly binning scheme leveraging sparse dictionary learning and matrix factorization to solve sparse decomposition problems arising in field of metagenomics. | Sparse dictionary learning, pre-assembly binning scheme, matrix factorization, sparse decomposition, metagenomic, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:Metagenomic_read_binning_using_sparse_coding | https://bio.tools/Metagenomic_read_binning_using_sparse_coding | SCR_018134 | Metagenomic_read_binning_using_sparse_coding | 2026-08-07 09:28:55 | 1 | |||||||
|
MEtabolomes, TRaits, and INteractions-Knowledge Graph Resource Report Resource Website 1+ mentions |
MEtabolomes, TRaits, and INteractions-Knowledge Graph (RRID:SCR_027914) | METRIN-KG | software resource, software toolkit, source code | Software pipeline for generating knowledge graph integrating emi, trydb, globi datasets. Code for constructing a knowledge graph that integrates enriched metabolite data from Experimental Natural Products Knowledge Graph (ENPKG), LOTUS (available through Wikidata), plant trait data from TRY, and biotic interaction data from Global Biotic Interactions (GloBI). It performs taxonomic alignment against Wikidata records and generates Resource Description Framework (RDF) triples representing taxonomic relationships, traits, and species interactions. The resulting knowledge graph is queryable via a SPARQL (SPARQL Protocol and RDF Query Language) endpoint. | Knowledge Graphs, Plant Metabolomes, Plant Traits, Biotic Interactions | is listed by: bio.tools | Swiss Open Research Data Grants (CHORD) in Open Science I ; Swiss National Science Foundation Anticipating the Chemistry of Life - IC00I0-227830; MetaDiv 315230_215724 MetaboLinkAI 10.002.786; Horizon Europe MICROBES-4-CLIMATE 101131818 |
DOI:10.1101/2025.08.20.671289 | Free, Available for download, Freely available, | https://bio.tools/metrin_kg | SCR_027914 | 2026-08-07 09:31:03 | 1 |
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