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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
AcroMine Resource Report Resource Website |
AcroMine (RRID:SCR_013196) | data access protocol, service resource, software resource, web service | An acronym dictionary which can be used to find distinct expanded forms of acronyms from MEDLINE. This freely available service can be used through your browser or by integrating it with your applications using the ReSTful service. Acromine identifies abbreviation definitions by assuming a word sequence co-occurring frequently with a parenthetical expression to be a potential expanded form. Applied to the whole MEDLINE (9,635,599 abstracts), the implemented system extracted 68,007 abbreviation candidates and recognized 467,402 expanded forms. The current Acromine achieves 99% precision and 82-95% recall on our evaluation corpus that roughly emulates the whole MEDLINE. | acronym, abbreviation, disambiguation, computational linguistics, text mining |
is listed by: FORCE11 is listed by: OMICtools has parent organization: University of Manchester; Manchester; United Kingdom |
JISC ; BBSRC ; EPSRC |
PMID:20360059 PMID:17050571 |
Free, Public | OMICS_01169, nif-0000-10215 | SCR_013196 | Acromine | 2026-09-19 12:52:39 | 0 | ||||||
|
CongrPE Resource Report Resource Website 1+ mentions |
CongrPE (RRID:SCR_013190) | CongrPE | software resource | A de novo assembly algorithm for Next-Generation Sequencing technology. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00011 | SCR_013190 | 2026-09-19 12:52:39 | 1 | ||||||||||
|
CallSim Resource Report Resource Website |
CallSim (RRID:SCR_013192) | CallSim | software resource | A software application that provides evidence for the validity of base calls believed to be sequencing errors and it is applicable to Ion Torrent and 454 data. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
Apache License | OMICS_01098 | SCR_013192 | CallSim - Low-volume read processing base corrector | 2026-09-19 12:52:39 | 0 | |||||||
|
SAPAS Resource Report Resource Website 50+ mentions |
SAPAS (RRID:SCR_013195) | SAPAS | software resource | A RNA-seq method for polyA research. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01413 | SCR_013195 | 2026-09-19 12:52:39 | 68 | ||||||||||
|
HMMSplicer Resource Report Resource Website 1+ mentions |
HMMSplicer (RRID:SCR_013315) | HMMSplicer | software resource | An accurate and efficient algorithm for discovering canonical and non-canonical splice junctions in short read datasets. |
is listed by: OMICtools has parent organization: University of California at San Francisco; California; USA |
OMICS_01241 | SCR_013315 | 2026-09-19 12:52:41 | 4 | ||||||||||
|
Trans-ABySS Resource Report Resource Website 50+ mentions |
Trans-ABySS (RRID:SCR_013322) | Trans-ABySS | software resource | A software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
OMICS_01326, biotools:trans-abyss | https://bio.tools/trans-abyss/ | SCR_013322 | 2026-09-19 12:52:41 | 72 | ||||||||
|
NEUMA Resource Report Resource Website 1+ mentions |
NEUMA (RRID:SCR_013324) | NEUMA | software resource | Software for estimating mRNA abundances from the whole transcriptome shotgun sequencing (RNA-Seq) data based on effective length normalization using uniquely mappable areas of gene and mRNA isoform models. Using the known transcriptome sequence model such as RefSeq, NEUMA pre-computes the numbers of all possible gene-wise and isoform-wise informative reads: the former being sequences mapped to all mRNA isoforms of a single gene exclusively and the latter uniquely mapped to a single mRNA isoform. The results are used to estimate the effective length of genes and transcripts, taking experimental distributions of fragment size into consideration. NEUMA covers a large proportion of genes and mRNA isoforms and offers a measure of consistency (''consistency coefficient'') for each gene between an independently measured gene-wise level and the sum of the isoform levels. NEUMA is applicable to both paired-end and single-end RNA-Seq data. |
is listed by: OMICtools has parent organization: Korea Research Institute of Bioscience and Biotechnology; Daejeon; South Korea |
PMID:21059678 | OMICS_01281 | SCR_013324 | Normalization by Expected Uniquely Mappable Area | 2026-09-19 12:52:41 | 5 | ||||||||
|
Probalign Resource Report Resource Website 10+ mentions |
Probalign (RRID:SCR_013332) | Probalign | alignment software, data processing software, image analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software that uses partition function posterior probability estimates to compute maximum expected accuracy multiple sequence alignments. Computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities.Produces accurate alignments on long and heterogeneous length datasets containing protein repeats. |
is used by: eProbalign is listed by: OMICtools is listed by: Debian has parent organization: New Jersey Institute of Technology; New Jersey; USA |
PMID:16954142 DOI:10.1093/bioinformatics/btl472 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00985 | https://sources.debian.org/src/probalign/ | SCR_013332 | Probalign: multiple sequence alignment using partition function posterior probabilities | 2026-09-19 12:52:41 | 16 | ||||||
|
RosettaDock Resource Report Resource Website 100+ mentions |
RosettaDock (RRID:SCR_013393) | RosettaDock | software resource | Predicts the structure of a protein-protein complex from the individual structures of the monomer components. |
is listed by: OMICtools has parent organization: Johns Hopkins University; Maryland; USA |
OMICS_01604 | SCR_013393 | 2026-09-19 12:52:42 | 125 | ||||||||||
|
ArrayOligoSelector Resource Report Resource Website 10+ mentions |
ArrayOligoSelector (RRID:SCR_013494) | ArrayOligoSelector | software resource | Software program to systematically design gene specific long oligonucleotide probes for entire genomes, for the purpose of developing whole genome microarrays. For each open reading frame, the program optimizes the oligo selection based upon several parameters, including uniqueness in the genome, sequence complexity, lack of self-binding, GC content and proximity to the 3''end of the gene. |
is listed by: OMICtools has parent organization: University of California at San Francisco; California; USA has parent organization: SourceForge |
PMID:12620119 | Free, Public, Commercial requires license, Use of the blat or gfclient options requires license | OMICS_00826 | SCR_013494 | 2026-09-19 12:52:43 | 13 | ||||||||
|
TreeView Resource Report Resource Website 1000+ mentions |
TreeView (RRID:SCR_013503) | TreeView | software resource | Software to graphically browse results of clustering and other analyses from Cluster. |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite has parent organization: University of California at Berkeley; Berkeley; USA |
DOI:10.1093/bioinformatics/bth349 | OMICS_01574 | https://sources.debian.org/src/treeview/ | SCR_013503 | 2026-09-19 12:52:43 | 2754 | ||||||||
|
ScanAlyze Resource Report Resource Website 10+ mentions |
ScanAlyze (RRID:SCR_013507) | ScanAlyze | software resource | Software to process fluorescent images of microarrays. |
is listed by: OMICtools has parent organization: University of California at Berkeley; Berkeley; USA |
OMICS_00846 | SCR_013507 | 2026-09-19 12:52:43 | 43 | ||||||||||
|
CNV-seq Resource Report Resource Website 100+ mentions |
CNV-seq (RRID:SCR_013357) | CNV-seq | software resource | A method for detecting DNA copy number variation (CNV) using high-throughput sequencing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:cnv-seq, OMICS_00339 | https://bio.tools/cnv-seq | SCR_013357 | 2026-09-19 12:52:41 | 167 | |||||||
|
MEDEA Resource Report Resource Website 100+ mentions |
MEDEA (RRID:SCR_013356) | MEDEA | software resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented June, 2019.Comparative Genomic Visualization with Adobe Flash. |
is listed by: OMICtools has parent organization: Broad Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00941 | SCR_013356 | 2026-09-19 12:52:41 | 119 | |||||||||
|
PiMS Resource Report Resource Website 100+ mentions |
PiMS (RRID:SCR_011816) | PiMS | software resource | Software for a Laboratory Information Management System (LIMS) developed to support the unpredictable workflows of Molecular biology and Protein production labs of all sizes. | protein | is listed by: OMICtools | BBSRC ; CCP4 ; Instruct |
PMID:21385349 | Free for academic use | OMICS_01010 | SCR_011816 | Protein Information Management System | 2026-09-19 12:52:19 | 190 | |||||
|
Annmap Resource Report Resource Website 1+ mentions |
Annmap (RRID:SCR_011783) | Annmap | data or information resource, database, software resource | A genome browser that includes mappings between genomic features and Affymetrix microarrays. Associated with annmap is: * a Bioconductor package, annmap that provides programmatic access to the underlying MySQL database tables (which are freely available for download on this site) * xmapbridge, a Bioconductor package that outputs numeric data in a form suitable for presentation in the browser. This is supported by XMapBridge, a Java client that sits on the local desktop and performs the graph rendering for the browser. | is listed by: OMICtools | Cancer Research UK ; Cancer Research UK Manchester Institute |
OMICS_00900 | SCR_011783 | 2026-09-19 12:52:18 | 6 | |||||||||
|
B-Fabric Resource Report Resource Website 1+ mentions |
B-Fabric (RRID:SCR_011827) | B-Fabric | data or information resource, data repository, database, service resource, storage service resource | An open infrastructure for managing projects and data in life sciences that allows to store and access experimental data together with its scientific context. The platform connects the data from scientific instruments with data analysis tools, including workflow, annotation, and data visualization support. All public data can be searched and used to carry out inter-experiment analyses. For a fee, B-Fabric Order allows you to order the following analytical services at the FGCZ independent of a User Lab research project: Mass spectrometry, Protein sequencing, peptide sequencing, Amino acid analysis, Chromatography, Electrophoresis. | project management, mass spectrometry, protein sequencing, peptide sequencing, amino acid analysis, chromatography, electrophoresis |
is listed by: OMICtools has parent organization: University of Zurich; Zurich; Switzerland |
PMID:21772064 | Account required | OMICS_01002 | SCR_011827 | 2026-09-19 12:52:19 | 1 | |||||||
|
Galaxy LIMS Resource Report Resource Website |
Galaxy LIMS (RRID:SCR_011829) | Galaxy LIMS | software resource | A laboratory information management system (LIMS) for a next-generation sequencing (NGS) laboratory within the existing Galaxy platform. | is listed by: OMICtools | BMBF | PMID:23479349 | OMICS_01004 | SCR_011829 | 2026-09-19 12:52:19 | 0 | ||||||||
|
GPU-BLAST Resource Report Resource Website |
GPU-BLAST (RRID:SCR_011820) | GPU-BLAST | software resource | Software for an accelerated version of the popular NCBI-BLAST using a general-purpose graphics processing unit (GPU). It s nearly four times faster, while producing identical results. GPU-BLAST supports: protein alignment according to blastp (it does not support psiblast), multiple CPU threads working in parallel with a single GPU, and input files with multiple protein queries. | c++, gpu/cuda |
is listed by: OMICtools has parent organization: Carnegie Mellon University; Pennsylvania; USA |
PMID:21088027 | Free, Public, Acknowledgement requested | OMICS_00995 | http://eudoxus.cheme.cmu.edu/gpublast/gpublast.html | SCR_011820 | 2026-09-19 12:52:19 | 0 | ||||||
|
TBLASTX Resource Report Resource Website 1000+ mentions |
TBLASTX (RRID:SCR_011823) | TBLASTX | software resource, web application | A web-based tool used to search translated nucleotide databases using a translated nucleotide query. | nucleotide database, web based, nucleotide query |
is listed by: OMICtools has parent organization: NCBI |
Available to the research community | OMICS_01000 | SCR_011823 | Translated BLAST: tblastx | 2026-09-19 12:52:19 | 1467 |
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