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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
DeNovoGUI Resource Report Resource Website 10+ mentions |
DeNovoGUI (RRID:SCR_012074) | software resource | Software providing a user-friendly and lightweight graphical user interface for running parallelized versions of the freely available de novo sequencing software PepNovo+, greatly simplifying the use of de novo sequencing in proteomics. |
is listed by: OMICtools has parent organization: Google Code |
PMID:24295440 | Apache License | OMICS_04546 | SCR_012074 | 2026-08-01 12:04:31 | 11 | |||||||||
|
kruX Resource Report Resource Website 1+ mentions |
kruX (RRID:SCR_012076) | software resource | An algorithm implemented in Matlab, Python and R that uses matrix multiplications to simultaneously calculate the Kruskal-Wallis test statistic for several millions of marker-trait combinations at once. | standalone software, matlab, python, r |
is listed by: OMICtools has parent organization: Google Code |
PMID:24423115 | GNU General Public License | OMICS_04593 | SCR_012076 | 2026-08-01 12:04:33 | 5 | ||||||||
|
SNP ratio test Resource Report Resource Website 1+ mentions |
SNP ratio test (RRID:SCR_012070) | software resource | Software to calculate the number of significant SNPs in pathway divided by the number of SNPs in pathway. | standalone software, perl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:19620097 | GNU General Public License | biotools:snp_ratio_test, OMICS_04390 | https://bio.tools/snp_ratio_test | SCR_012070 | 2026-08-01 12:04:33 | 2 | |||||||
|
compomics-utilities Resource Report Resource Website 1+ mentions |
compomics-utilities (RRID:SCR_012073) | software resource | A software library containing code shared by many research projects, amongst others containing panels for visualizing spectra and chromatograms and objects for representing peptides and proteins etc. This library can be of use to other research groups doing computational proteomics. | standalone software, java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:21385435 | Apache License, v2 | OMICS_04545, biotools:compomics-utilities | https://bio.tools/compomics-utilities | SCR_012073 | 2026-08-01 12:04:33 | 5 | |||||||
|
CAMPways Resource Report Resource Website 1+ mentions |
CAMPways (RRID:SCR_012072) | software resource | Software that provides one-to-many alignments of reactions in a pair of metabolic pathways. | standalone software |
is listed by: OMICtools has parent organization: Google Code |
PMID:23812978 | OMICS_04907 | SCR_012072 | 2026-08-01 12:04:31 | 1 | |||||||||
|
Toxtree Resource Report Resource Website 50+ mentions |
Toxtree (RRID:SCR_012086) | software resource | A full-featured and flexible user-friendly open source software application, which is able to estimate toxic hazard by applying a decision tree approach. | standalone software, web app |
is listed by: OMICtools has parent organization: SourceForge |
PMID:18853299 | OMICS_05024 | SCR_012086 | 2026-08-01 12:04:33 | 95 | |||||||||
|
Viewmol Resource Report Resource Website |
Viewmol (RRID:SCR_012088) | software resource | Software providing a graphical front end for computational chemistry programs. | standalone software, windows, c, python |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
GNU General Public License | OMICS_05057 | https://sources.debian.org/src/viewmol/ | SCR_012088 | 2026-08-01 12:04:35 | 0 | ||||||||
|
Toxmatch Resource Report Resource Website 1+ mentions |
Toxmatch (RRID:SCR_012087) | software resource | A software tool to facilitate chemical similarity calculations. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:18617309 | OMICS_05025 | SCR_012087 | 2026-08-01 12:04:32 | 2 | |||||||||
|
QuteMol Resource Report Resource Website 10+ mentions |
QuteMol (RRID:SCR_012089) | software resource | Open source (GPL) software providing an interactive, high quality molecular visualization system. | standalone software, unix/linux, windows |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:17080857 DOI:10.1109/TVCG.2006.115 |
Free, Freely available | OMICS_05075 | https://sources.debian.org/src/qutemol/ | SCR_012089 | 2026-08-01 12:04:32 | 13 | |||||||
|
ExpressionView Resource Report Resource Website |
ExpressionView (RRID:SCR_012004) | ExpressionView | software resource | An R package that provides an interactive environment to explore biclusters identified in gene expression data. | is listed by: OMICtools | PMID:20671149 | Free | OMICS_01800 | SCR_012004 | ExpressionView - Visualize biclusters identified in gene expression data | 2026-08-01 12:04:32 | 0 | |||||||
|
BiBench Resource Report Resource Website |
BiBench (RRID:SCR_012003) | BiBench | software resource | A Python library designed to simplify biclustering tasks. | is listed by: OMICtools | OMICS_01798 | SCR_012003 | 2026-08-01 12:04:28 | 0 | ||||||||||
|
Pride-asap Resource Report Resource Website 1+ mentions |
Pride-asap (RRID:SCR_012052) | software resource | An open source software application and library written in Java that provides a uniform annotation of identified spectra stored in the PRIDE database. | standalone software, java |
is listed by: OMICtools has parent organization: Google Code |
PMID:23603108 | OMICS_03348 | SCR_012052 | 2026-08-01 12:04:33 | 9 | |||||||||
|
XTandem Parser Resource Report Resource Website |
XTandem Parser (RRID:SCR_012055) | software resource | An open-source Java library that parses X!Tandem XML result files into an easily accessible and fully functional object model. | standalone software, java |
is listed by: OMICtools is related to: X!Tandem is related to: X!Tandem has parent organization: Google Code |
PMID:20140905 | Apache License | OMICS_03353 | SCR_012055 | 2026-08-01 12:04:33 | 0 | ||||||||
|
Maltcms Resource Report Resource Website |
Maltcms (RRID:SCR_012057) | software resource | An application framework mainly suited for developers working in the domain of bioinformatics for metabolomics and proteomics. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_03356 | SCR_012057 | Modular Application Toolkit for Chromatography Mass-Spectrometry | 2026-08-01 12:04:35 | 0 | ||||||||||
|
PRIDE Converter 2 Resource Report Resource Website |
PRIDE Converter 2 (RRID:SCR_012051) | software resource | Suite of software tools that allows users to convert search result files into PRIDE XML, generate mzTab skeleton files that can be used as a basis to submit quantitative and gel-based MS data, and post-process PRIDE XML files by filtering out contaminants and empty spectra. | standalone software, mac os x, unix/linux, windows, java, xml, mass spectrometry, pride, ols, proteomics, psi, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: ISA Infrastructure for Managing Experimental Metadata has parent organization: Google Code |
PMID:22949509 | Apache License, v2 | biotools:pride_converter, OMICS_03344 | https://bio.tools/pride_converter | SCR_012051 | PRIDE, PRoteomics IDEntification (PRIDE) Converter 2 | 2026-08-01 12:04:30 | 0 | ||||||
|
jmzReader Resource Report Resource Website 1+ mentions |
jmzReader (RRID:SCR_012050) | software resource | A collection of Java application programming interfaces (APIs) to parse the most commonly used peak list and XML-based mass spectrometry (MS) data formats: DTA, MS2, MGF, PKL, mzXML, mzData, and mzML. | standalone software, mac os x, unix/linux, windows, java |
is listed by: OMICtools has parent organization: Google Code |
PMID:22539430 | Apache License | OMICS_03341 | SCR_012050 | 2026-08-01 12:04:30 | 2 | ||||||||
|
FIGG Resource Report Resource Website 1+ mentions |
FIGG (RRID:SCR_012064) | software resource | A large-scale whole genome simulation tool which generates large numbers of whole genomes with known sequence characteristics based on direct sampling of experimentally known or theorized variations. | standalone software, unix/linux, mac os x, windows, java, mapreduce |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24885193 | Free, Public | OMICS_04164 | SCR_012064 | Frequency-based Insilico Genome Generator | 2026-08-01 12:04:31 | 3 | |||||||
|
DIYA Resource Report Resource Website 10+ mentions |
DIYA (RRID:SCR_012066) | software resource | A modular and configurable open source pipeline software, written in Perl, used for the rapid annotation of bacterial genome sequences. | standalone software, c++, java, perl, python |
is listed by: OMICtools has parent organization: SourceForge |
PMID:19254921 | GNU General Public License | OMICS_04221 | SCR_012066 | Do-It-Yourself Annotator | 2026-08-01 12:04:35 | 10 | |||||||
|
Fastphylo Resource Report Resource Website 1+ mentions |
Fastphylo (RRID:SCR_012068) | software resource | A software package containing implementations of efficient algorithms for two common problems in phylogenetics: estimating DNA/protein sequence distances and reconstructing a phylogeny from a distance matrix. | applet |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24255987 | OMICS_04248 | SCR_012068 | 2026-08-01 12:04:31 | 2 | |||||||||
|
MrBayes Resource Report Resource Website 10000+ mentions |
MrBayes (RRID:SCR_012067) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on February 28,2023. Software program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. | applet, mac os x, unix/linux, windows |
is listed by: OMICtools is listed by: SoftCite has parent organization: SourceForge |
PMID:22357727 DOI:10.1093/sysbio/sys029 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04237 | https://sources.debian.org/src/mrbayes/ | SCR_012067 | 2026-08-01 12:04:33 | 10711 |
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