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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
netClass Resource Report Resource Website |
netClass (RRID:SCR_005672) | netClass | software resource | An R package for network-based feature (gene) selection for biomarkers discovery via integrating biological information. The package adapts the following 5 algorithms for classifying and predicting gene expression data using prior knowledge: # average gene expression of pathway (aep); # pathway activities classification (PAC); # Hub network classification (hubc); # filter via top ranked genes (FrSVM); # network smoothed t-statistic (stSVM). | protein-protein interaction network, biomarker discovery, classification, micoarray, gene expression profile, protein-protein interaction, gene expression, gene, biomarker |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24443376 | Free, Public | OMICS_02241 | SCR_005672 | 2026-08-01 12:03:01 | 0 | |||||||
|
DMRforPairs Resource Report Resource Website 1+ mentions |
DMRforPairs (RRID:SCR_005702) | software resource | Software for identifying differentially methylated regions between unique samples using array based methylation profiles. It allows researchers to compare n greater than or equal to 2 unique samples with regard to their methylation profile. The (pairwise) comparison of n unique single samples distinguishesit from other existing pipelines as these often compare groups of samples in either single CpG locus or region based analysis. DMRforPairs defines regions of interest as genomic ranges with sufficient probes located in close proximity to each other. Probes in one region are optionally annotated to the same functional class(es). Differential methylation is evaluated by comparing the methylation values within each region between individual samples and (if the difference is sufficiently large), testing this difference formally for statistical significance. | standalone software, mac os x, unix/linux, windows, r, annotation, dna methylation, differential methylation, microarray, report writing, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:24884391 | GNU General Public License, v2 or greater | biotools:dmrforpairs, OMICS_04059 | https://bio.tools/dmrforpairs | SCR_005702 | DMR2+, DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles | 2026-08-01 12:03:01 | 4 | ||||||
|
VAGUE Resource Report Resource Website 1+ mentions |
VAGUE (RRID:SCR_005607) | VAGUE | software resource | An open-source de novo genome assembly software tool, which is run from the Unix command line, providing a multi-platform graphical front-end for the Velvet de novo assembler. VAGUE is implemented in JRuby and targets the Java Virtual Machine. | command line, assembler |
is listed by: OMICtools has parent organization: Monash University; Melbourne; Australia |
PMID:23162059 | GNU General Public License, v2, Acknowledgement requested | OMICS_00897 | SCR_005607 | Velvet Assembler Graphical Front End | 2026-08-01 12:02:55 | 5 | ||||||
|
Bismark Resource Report Resource Website 1000+ mentions |
Bismark (RRID:SCR_005604) | Bismark | software resource | Software tool to map bisulfite converted sequence reads and determine cytosine methylation states. Flexible aligner and methylation caller for Bisulfite-Seq applications. Used to map bisulfite treated sequencing reads to genome of interest and perform methylation calls in single step. | Map bisulfite treated sequence reads, determine cytosine methylation states, genome, sequence reads, perform methylation calls, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Babraham Institute |
PMID:21493656 DOI:10.1093/bioinformatics/btr167 |
Free, Available for download, Freely available | biotools:bismark, OMICS_00575 | https://github.com/FelixKrueger/Bismark, https://bio.tools/bismark | https://sources.debian.org/src/bismark/ | SCR_005604 | 2026-08-01 12:02:55 | 1123 | |||||
|
jMHC Resource Report Resource Website 10+ mentions |
jMHC (RRID:SCR_005605) | jMHC | software resource | Software for analyzing and visualization of the results of deep amplicon sequencing. | matlab |
is listed by: OMICtools has parent organization: Google Code |
PMID:21676201 | GNU General Public License, v3, Acknowledgement requested | OMICS_00300 | SCR_005605 | jmhc - software for analyzing and visualization of the results of deep amplicon sequencing | 2026-08-01 12:02:56 | 10 | ||||||
|
TMA-Combiner Resource Report Resource Website 1+ mentions |
TMA-Combiner (RRID:SCR_005600) | TMA-Combiner | software resource | A Simple Software Tool to Permit Analysis of Replicate Cores on Tissue Microarrays., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | tissue microarray |
is listed by: OMICtools is related to: Stanford TMA Software has parent organization: Stanford University; Stanford; California |
PMID:16258508 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00822 | SCR_005600 | 2026-08-01 12:03:00 | 1 | |||||||
|
TMAJ Resource Report Resource Website 10+ mentions |
TMAJ (RRID:SCR_005601) | TMAJ | software resource | Open-source software to support information and images related to tissue micro-arrays. It contains support for multiple organ systems, multiple users, image analysis, and is designed to be compliant with HIPPA regulations. Patients, specimens, blocks, slides, cores, images, and scores can all be stored and viewed. Features include advanced security, custom dynamic fields, and an image analysis program. | tissue microarray, java, java swing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Johns Hopkins University; Maryland; USA has parent organization: SourceForge |
GNU General Public License, v3 | biotools:tmaj, OMICS_00823 | https://bio.tools/tmaj | SCR_005601 | TMAJ Software Project | 2026-08-01 12:02:55 | 10 | ||||||
|
GOProfiler Resource Report Resource Website 1+ mentions |
GOProfiler (RRID:SCR_005683) | GOProfiler | service resource | Service that provides a summary of GO annotations available for each species. The user provides a taxon id and GOProfiler displays the number of GO associations and the number of annotated proteins for that species. The results are listed by evidence code and a separate list of unannotated proteins is also provided. | ontology or annotation browser, annotation, protein, gene ontology |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology has parent organization: AgBase |
PMID:16961921 | Free for academic use | OMICS_02269, nlx_149127 | SCR_005683 | 2026-08-01 12:03:01 | 2 | |||||||
|
Stanford TMA Software Resource Report Resource Website 1+ mentions |
Stanford TMA Software (RRID:SCR_005598) | Stanford TMA | software resource | Software Tools for High-Throughput Analysis and Archiving of Immunohistochemistry Staining Data Obtained with Tissue Microarrays. | tissue microarray |
is listed by: OMICtools is related to: TMA-Combiner has parent organization: Stanford University; Stanford; California |
PMID:12414504 | OMICS_00819 | SCR_005598 | Stanford TMA Software website, Stanford Tissue Microarray Software | 2026-08-01 12:02:56 | 1 | |||||||
|
OXBench Resource Report Resource Website 1+ mentions |
OXBench (RRID:SCR_005591) | OXBench | software resource | A suite of programs aimed at developers of alignment methods rather than end-users to assess the accuracy of multiple sequence alignment methods. It includes a reference database of protein multiple sequence alignments that were generated by consideration of protein three-dimensional structure. | alignment, linux, protein, sequence alignment |
is listed by: OMICtools has parent organization: University of Dundee; Scotland; United Kingdom |
PMID:14552658 | Acknowledgement requested | OMICS_00983 | http://www.compbio.dundee.ac.uk/Software/Oxbench/oxbench.html Alt. URL: http://www.compbio.dundee.ac.uk/software.html | SCR_005591 | 2026-08-01 12:02:55 | 2 | ||||||
|
Staden Package Resource Report Resource Website 50+ mentions |
Staden Package (RRID:SCR_005629) | software resource | A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows. | c, unix/linux, sequence assembly, dna/protein analysis, spin, sequence alignment, genome, genome viewer, c++, fortran, tcl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:20513662 DOI:10.1093/bioinformatics/btq268 |
BSD License | OMICS_00894, biotools:staden | https://bio.tools/staden, https://sources.debian.org/src/staden/ | SCR_005629 | Staden Package | 2026-08-01 12:02:57 | 79 | ||||||
|
Chromaseq Resource Report Resource Website 1+ mentions |
Chromaseq (RRID:SCR_005587) | Chromaseq | software resource | A software package in Mesquite that processes chromatograms, makes contigs, base calls, etc., using in part the programs Phred and Phrap. | chromatogram, sequence, mesquite |
is listed by: OMICtools has parent organization: Oregon State University; Oregon; USA |
NSF EF-0531754 | Acknowledgement required | OMICS_01017 | SCR_005587 | Chromaseq: a package for processing chromatograms and sequence data in Mesquite | 2026-08-01 12:02:55 | 7 | ||||||
|
snp-search Resource Report Resource Website |
snp-search (RRID:SCR_005618) | snp-search | software resource | A software tool that manages SNP data and outputs useful information which can be used to test important biological hypotheses. | is listed by: OMICtools | PMID:24246037 | OMICS_00303 | SCR_005618 | 2026-08-01 12:02:55 | 0 | |||||||||
|
diCal-IBD Resource Report Resource Website |
diCal-IBD (RRID:SCR_012111) | software resource | Software tool for detecting identity-by-descent (IBD) tracts between pairs of genomic sequences. | standalone software, unix/linux, mac os x, windows, python |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25147361 | BSD License | OMICS_05459 | SCR_012111 | 2026-08-01 12:04:35 | 0 | ||||||||
|
Ionwinze Resource Report Resource Website |
Ionwinze (RRID:SCR_012115) | software resource | Software tool to pick out ion signals that discriminate two groups of samples (e.g. diseased/healthy, resistant/susceptible) by quasi-datapoint-wise comparison using univariate statistic procedures. | standalone software, windows, c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24004415 | GNU General Public License | OMICS_05522 | SCR_012115 | 2026-08-01 12:04:34 | 0 | ||||||||
|
GenoSIGHT Resource Report Resource Website |
GenoSIGHT (RRID:SCR_012119) | software resource | An adaptive imaging cytometry software environment. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25210731 | OMICS_05634 | SCR_012119 | 2026-08-01 12:04:34 | 0 | |||||||||
|
MSImageViewer Resource Report Resource Website |
MSImageViewer (RRID:SCR_012121) | software resource | Software for the conversion of data acquired with the FlashQuant (MALDI version of ABSciex 4000) into MS images. | standalone software | is listed by: OMICtools | Free, Public | OMICS_05672 | SCR_012121 | 2026-08-01 12:04:36 | 0 | |||||||||
|
Cell motility Resource Report Resource Website |
Cell motility (RRID:SCR_012120) | software resource | An open source Java application that provides a clear and concise analysis workbench for large amounts of cell motion data. | applet, java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:16762054 | Apache License, v2 | biotools:cell-motility, OMICS_05660 | https://bio.tools/cell-motility | SCR_012120 | Cell_motility | 2026-08-01 12:04:34 | 0 | ||||||
|
GlycanBuilder Resource Report Resource Website 1+ mentions |
GlycanBuilder (RRID:SCR_012123) | software resource | An intuitive and flexible software tool for building and displaying glycan structures. | standalone software |
is listed by: OMICtools has parent organization: Google Code |
PMID:23109548 | GNU Lesser General Public License | OMICS_05681 | SCR_012123 | 2026-08-01 12:04:34 | 6 | ||||||||
|
GlycReSoft Resource Report Resource Website 10+ mentions |
GlycReSoft (RRID:SCR_012122) | software resource | A software package for automated recognition of glycans from LC/MS data. | software package |
is listed by: OMICtools has parent organization: Google Code |
PMID:23049804 | GNU General Public License | OMICS_05674 | SCR_012122 | 2026-08-01 12:04:34 | 27 |
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