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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
GARM Resource Report Resource Website 10+ mentions |
GARM (RRID:SCR_006731) | GARM | software resource | A new software pipeline to merge and reconcile assemblies from different algorithms or sequencing technologies. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01420 | SCR_006731 | Genome Assembler Reconcilation and Merging | 2026-08-01 12:03:15 | 11 | |||||||||
|
FLUX CAPACITOR Resource Report Resource Website 1+ mentions |
FLUX CAPACITOR (RRID:SCR_006651) | FLUX CAPACITOR | software resource | Software to recontruct abundances of known transcript forms from RNAseq data. The algorithm works by distributing the reads mapping to a given exonic region (or splice junction) among the transcripts including the exon (or splice junction). The input is the annotation of a reference transcriptome and reads from RNAseq technologies aligned to the genome. From the reference annotation, splicing graphs are produced and reads are mapped to corresponding edges in these graphs according to the position where they align in the genomic sequence. The resulting graph with edges labelled by the number of reads can be interpreted as a flow network where each transcript representing a transportation path from its start to its end and consequently each edge a possibly shared segment of transportation along which a certain number of reads per nucleotide -- i.e., a flux -- is observed. Given a density function of reads along a transcript, the expected participation of each transcript in an edge under consideration can be estimated. The basic idea is to cast back from these latter participations and the observed number of reads - allowing for a certain amount of noise - to the original transcript abundancies. To do so, a linear constraint is formalized for each edge, and an optimal solution for the complete set of constraints is found by a standard linear program solver. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:20220756 | biotools:the_flux_capacitor, OMICS_01293 | https://bio.tools/the_flux_capacitor | SCR_006651 | The FLUX CAPACITOR, FluxCapacitor | 2026-08-01 12:03:14 | 2 | ||||||
|
TIGAR Resource Report Resource Website 10+ mentions |
TIGAR (RRID:SCR_006650) | TIGAR | software resource | Software to estimate transcript isoform abundances from RNA-Seq data by variational Bayesian inference. The statistical method can handle gapped alignments of reads against reference sequences so that it allows insertion or deletion errors within reads. | is listed by: OMICtools | PMID:23821651 | OMICS_01294 | SCR_006650 | TIGAR: Transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference | 2026-08-01 12:03:17 | 43 | ||||||||
|
APOLLOH Resource Report Resource Website 10+ mentions |
APOLLOH (RRID:SCR_006648) | APOLLOH | software resource | A hidden Markov model (HMM) for predicting somatic loss of heterozygosity and allelic imbalance in whole tumour genome sequencing data. |
is listed by: OMICtools has parent organization: BC Cancer Agency |
OMICS_00306 | SCR_006648 | 2026-08-01 12:03:14 | 21 | ||||||||||
|
openBIS Resource Report Resource Website 10+ mentions |
openBIS (RRID:SCR_011815) | openBIS | software resource | Software for an open, distributed system for managing biological information that supports biological research data workflows from the source (i.e. the measurement instruments) to facilitate the process of answering biological questions by means of cross-domain queries against raw data, processed data, knowledge resources and its corresponding metadata. The openBIS software framework can be easily extended and has been customized for the following technologies: * High Content Screening * Proteomics * Deep Sequencing * Metabolomics |
is listed by: OMICtools has parent organization: ETH Zurich; Zurich; Switzerland |
PMID:22151573 | OMICS_01009 | SCR_011815 | open Biology Information System | 2026-08-01 12:04:19 | 13 | ||||||||
|
Kalign Resource Report Resource Website 100+ mentions |
Kalign (RRID:SCR_011810) | Kalign | software resource | A fast and accurate multiple sequence alignment algorithm. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: European Bioinformatics Institute |
PMID:16343337 DOI:10.1093/bioinformatics/btz795 |
Free | OMICS_00978, biotools:kalign | https://bio.tools/kalign, https://sources.debian.org/src/kalign/ | SCR_011810 | 2026-08-01 12:04:19 | 119 | ||||||
|
CGView Resource Report Resource Website 100+ mentions |
CGView (RRID:SCR_011779) | CGView | software resource | A Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web., 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 is listed by: SoftCite has parent organization: University of Alberta; Alberta; Canada |
DOI:10.1093/bioinformatics/bti054 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00905, biotools:cgview | https://bio.tools/cgview, https://sources.debian.org/src/cgview/ | SCR_011779 | Circular Genome Viewer | 2026-08-01 12:04:17 | 304 | |||||
|
PSAR-Align Resource Report Resource Website 1+ mentions |
PSAR-Align (RRID:SCR_011814) | PSAR-Align | software resource | Software for improving multiple sequence alignment using probabilistic sampling. | c++, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24222208 | Free | OMICS_00987, biotools:psar | https://bio.tools/psar | SCR_011814 | PSAR-Align: improving multiple sequence alignment using probabilistic sampling | 2026-08-01 12:04:30 | 1 | |||||
|
Gaggle Resource Report Resource Website |
Gaggle (RRID:SCR_011780) | Gaggle | software resource | An open source software tool for visualizing high-density data plotted against coordinates on the genome. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Open unspecified license, Free | biotools:ggb, OMICS_00909 | https://bio.tools/ggb | SCR_011780 | 2026-08-01 12:04:18 | 0 | |||||||
|
HiTEC Resource Report Resource Website 1+ mentions |
HiTEC (RRID:SCR_011826) | HiTEC | software resource | Accurate error correction in high-throughput sequencing data. | is listed by: OMICtools | OMICS_01105 | SCR_011826 | 2026-08-01 12:04:20 | 6 | ||||||||||
|
PatMaN Resource Report Resource Website 50+ mentions |
PatMaN (RRID:SCR_011821) | PatMaN | software resource | Software that searches for short patterns in large DNA databases, allowing for approximate matches., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | c++, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:18467344 DOI:10.1093/bioinformatics/btn223 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00997, biotools:patman | https://bio.tools/patman, https://sources.debian.org/src/patman/ | SCR_011821 | PatMaN - A DNA pattern matcher for short sequences | 2026-08-01 12:04:30 | 61 | |||||
|
Hammer Resource Report Resource Website 100+ mentions |
Hammer (RRID:SCR_011825) | Hammer | software resource | A tool for error correction of short read datasets with non-uniform coverage, such as single-cell data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools has parent organization: University of California at San Diego; California; USA |
PMID:21685062 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01103 | SCR_011825 | Hammer: error correction with non-uniform coverage | 2026-08-01 12:04:19 | 196 | |||||||
|
Infernal Resource Report Resource Website 500+ mentions |
Infernal (RRID:SCR_011809) | Infernal | software resource | Software for searching DNA sequence databases for RNA structure and sequence similarities. | FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite is related to: ANNOgesic has parent organization: Janelia Research |
PMID:24008419 DOI:10.1093/bioinformatics/btp157 |
GNU General Public License, v3 | OMICS_00977 | https://sources.debian.org/src/infernal/ | SCR_011809 | Infernal: inference of RNA alignments, INFERence of RNA Alignment | 2026-08-01 12:04:19 | 687 | |||||
|
GenomeMatcher Resource Report Resource Website 50+ mentions |
GenomeMatcher (RRID:SCR_011800) | GenomeMatcher | software resource | A graphical interface for comparative genomics. | is listed by: OMICtools | OMICS_00936 | SCR_011800 | 2026-08-01 12:04:32 | 61 | ||||||||||
|
GenomeRing Resource Report Resource Website 1+ mentions |
GenomeRing (RRID:SCR_011801) | GenomeRing | software resource | Alignment visualization based on SuperGenome coordinates. |
is listed by: OMICtools has parent organization: University of Tubingen; Tubingen; Germany |
OMICS_00937 | SCR_011801 | 2026-08-01 12:04:18 | 2 | ||||||||||
|
Gobe Resource Report Resource Website 1+ mentions |
Gobe (RRID:SCR_011802) | Gobe | software resource | An interactive, web-based tool for comparative genomic visualization. | is listed by: OMICtools | OMICS_00938 | SCR_011802 | 2026-08-01 12:04:30 | 2 | ||||||||||
|
GSV Resource Report Resource Website 1+ mentions |
GSV (RRID:SCR_011803) | GSV | software resource | Software that allows users to upload files which contain synteny regions between two or more genomes and interactively visualize the synteny between them. | is listed by: OMICtools | OMICS_00939 | SCR_011803 | Genome Synteny Viewer | 2026-08-01 12:04:19 | 2 | |||||||||
|
UTGB Toolkit Resource Report Resource Website 1+ mentions |
UTGB Toolkit (RRID:SCR_011797) | UTGB Toolkit | software resource | An open-source software for developing personalized genome browsers that work in web browsers. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Tokyo; Tokyo; Japan |
Open unspecified license | OMICS_00927, biotools:utgb_toolkit | https://bio.tools/utgb_toolkit | SCR_011797 | University of Tokyo Genome Browser | 2026-08-01 12:04:18 | 1 | ||||||
|
Btrim Resource Report Resource Website 50+ mentions |
Btrim (RRID:SCR_011836) | Btrim | software resource | A fast and lightweight software to trim adapters and low quality regions in reads from ultra high-throughput next-generation sequencing machines. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Yale School of Medicine; Connecticut; USA |
PMID:21651976 | biotools:btrim, OMICS_01083 | https://bio.tools/btrim | SCR_011836 | 2026-08-01 12:04:30 | 86 | |||||||
|
QuorUM Resource Report Resource Website 10+ mentions |
QuorUM (RRID:SCR_011840) | QuorUM | software resource | Software tool as error corrector for Illumina reads. It is distributed and used with MaSuRCA, or it can be used independently. |
is listed by: OMICtools is listed by: Debian has parent organization: University of Maryland; Maryland; USA |
DOI:10.1371/journal.pone.0130821 | OMICS_01107 | https://sources.debian.org/src/quorum/ | SCR_011840 | 2026-08-01 12:04:32 | 32 |
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