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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Queens University; Ontario; Canada Resource Report Resource Website |
Queens University; Ontario; Canada (RRID:SCR_000278) | university | Public university in Ontario, Canada that offers degree programs in the social sciences and engineering at both the undergraduate, graduate, postdoctorate and professional level. The university operates six research centers that focus on disciplines such as neuroscience, computing, human mobility and Southern African research. | ontario, canada, public, social science, engineering, professional degrees, undergraduate, graduate, masters, neuroscience |
is parent organization of: BLIMP: Biomedical LIterature Mining Publications is parent organization of: F-SNP: a collection of functional SNPs, specifically prioritized for disease association studies is parent organization of: Kinarm End-Point Lab |
grid.410356.5, ISNI:0000 0004 1936 8331, SCR_017061, Crossref funder ID:501100003321, Wikidata:Q1420038, nlx_63241 | https://ror.org/02y72wh86 | SCR_000278 | Queen's College at Kingston, Queens University; Kingston; Canada | 2026-02-14 01:59:40 | 0 | ||||||||
|
RNASeqReadSimulator Resource Report Resource Website 1+ mentions |
RNASeqReadSimulator (RRID:SCR_000270) | RNASeqReadSimulator | software resource | A software tool to generate simulated single-end or paired-end RNA-Seq reads. # It allows users to randomly assign expression levels of transcripts and generate simulated single-end or paired-end RNA-Seq reads. # It is able to generate RNA-Seq reads that have a specified positional bias profile. # It is able to simulate random read errors from sequencing platforms. # The simulator consists of a few simple Python scripts. All scripts are command line driven, allowing users to invoke and design more functions. | rna-seq, command line | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_01964 | SCR_000270 | 2026-02-14 01:59:41 | 1 | ||||||||
|
UW Department of Biochemistry Resource Report Resource Website |
UW Department of Biochemistry (RRID:SCR_000149) | university | A department within the University of Washington which focuses on both undergraduate and postgraduate education in biochemistry. | biochemistry, undergraduate, graduate, university, washington | has parent organization: University of Washington; Seattle; USA | Public, Academic | nlx_149153 | SCR_000149 | University of Washington Department of Biochemistry, UW Department of Biochemistry | 2026-02-14 01:59:37 | 0 | ||||||||
|
EdgeBio Resource Report Resource Website |
EdgeBio (RRID:SCR_000183) | EdgeBio | commercial organization | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A contract research organization that provides genomics services such as sequencing, bioinformatics, NGS data analysis and whole exome sequencing. EdgeBio is a CLIA-approved service provider. | contract research organization, CRO, genomics, genome, sequencing, bioinformatics, NGS data analysis, whole exome sequencing, research, Illumina NGS | is listed by: ScienceExchange | THIS RESOURCE IS NO LONGER IN SERVICE | SciEx_203 | https://www.edgebio.com/ | SCR_000183 | Edge Bio, EdgeBio.com | 2026-02-14 01:59:38 | 0 | ||||||
|
MIMOSA Resource Report Resource Website |
MIMOSA (RRID:SCR_000184) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for modeling count data using Dirichlet-multinomial and beta-binomial mixtures with applications to single-cell assays. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23887981 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mimosa, OMICS_05642 | https://bio.tools/mimosa | SCR_000184 | MIMOSA - Mixture Models for Single-Cell Assays, MIMOSA: Mixture Models For Single Cell Assays | 2026-02-14 01:59:38 | 0 | ||||||
|
MODENT - A Tool For Reconstructing Gene Regulatory Networks Resource Report Resource Website 1+ mentions |
MODENT - A Tool For Reconstructing Gene Regulatory Networks (RRID:SCR_000220) | ModEnt | software resource | A computational tool that reconstructs gene regulatory networks from high throughput experimental data. | gene regulatory network, experimental data, computation, computational tool, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Tel Aviv University; Ramat Aviv; Israel |
PMID:22216865 | Free, Available for download, Freely available | biotools:modent, OMICS_01685 | https://bio.tools/modent | SCR_000220 | 2026-02-14 01:59:39 | 1 | ||||||
|
GOLD Resource Report Resource Website 10+ mentions |
GOLD (RRID:SCR_000188) | GOLD | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software for virtual screening and identifying the binding mode of active molecules. It is comprehensively validated, widely used, and allows for high database enrichments. The software utilizes a novel methodology which avoids computationally expensive sequential docking of ligands into multiple protein structures. | virtual screening, binding, active molecules, ligand-protein bonding, computation, protein structures, lead optimization |
is listed by: OMICtools is listed by: SoftCite |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01602 | SCR_000188 | 2026-02-14 01:59:38 | 18 | ||||||||
|
Context Likelihood of Relatedness Resource Report Resource Website 1+ mentions |
Context Likelihood of Relatedness (RRID:SCR_000216) | CLR | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software that infers regulatory interactions between transcription factors and their targets using a compendium of gene expression profiles. | transcription factors, gene expression profile, regulatory interactions, likelihood, relatedness | is listed by: OMICtools | PMID:17214507 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01682 | http://gardnerlab.bu.edu/software&tools.html, | SCR_000216 | 2026-02-14 01:59:39 | 1 | ||||||
|
Council for Scientific and Industrial Research; Gauteng; South Africa Resource Report Resource Website 1+ mentions |
Council for Scientific and Industrial Research; Gauteng; South Africa (RRID:SCR_000214) | CSIR | nonprofit organization | A leading scientific and technology research, development and implementation organization in Africa that undertakes directed research and development for socio-economic growth and improving the quality of life of South African citizens. | south africa, global economy, south african parliament, quality of life | is related to: Pharma-Planta Consortium | nlx_158309, Crossref funder ID: 501100001332, ISNI: 0000 0004 0607 1766, grid.7327.1, Wikidata: Q849145 | https://ror.org/05j00sr48 | SCR_000214 | CSIR South Africa, Council for Scientific and Industrial Research | 2026-02-14 01:59:39 | 3 | |||||||
|
GENIE3 Resource Report Resource Website 10+ mentions |
GENIE3 (RRID:SCR_000217) | GENIE3 | software resource | An algorithm for the inference of gene regulatory networks from expression data. | javascript, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:20927193 | Free, Available for download, Freely available | biotools:genie3, OMICS_01683 | https://bio.tools/genie3 | http://www.montefiore.ulg.ac.be/~huynh-thu/software.html | SCR_000217 | 2026-02-14 01:59:39 | 10 | |||||
|
Inferelator Resource Report Resource Website 1+ mentions |
Inferelator (RRID:SCR_000218) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Algorithm for learning parsimonious regulatory networks from systems biology data sets de novo. Software that utilizes inference algorithm to model genetic regulatory networks.Inferelator 2.0 is scalable framework for reconstruction of dynamic regulatory network models., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | modeling, inference algorithm, halobacterium, genetic regulatory network, learning regulatory network, model gene regulatory network | is listed by: OMICtools | PMID:23525069 PMID:16686963 PMID:19964678 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01684 | SCR_000218 | 2026-02-14 01:59:39 | 3 | ||||||||
|
c3net Resource Report Resource Website 1+ mentions |
c3net (RRID:SCR_000212) | software resource | Software package that allows inferring gene regulatory networks with direct physical interactions from microarray expression data using C3NET. | gene regulation, microarray expression, c3net | is listed by: OMICtools | PMID:20920161 | Free, Available for download, Freely available | OMICS_01681 | SCR_000212 | 2026-02-14 01:59:38 | 4 | ||||||||
|
GraBCas Resource Report Resource Website |
GraBCas (RRID:SCR_000205) | GraBCas | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software tool for predicting granzyme B and caspase cleavage sites. | matlab, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:15980455 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01674, biotools:grabcas | https://bio.tools/grabcas | SCR_000205 | 2026-02-14 01:59:38 | 0 | ||||||
|
GPS-Calpain Cleavage Detector Resource Report Resource Website 1+ mentions |
GPS-Calpain Cleavage Detector (RRID:SCR_000202) | GPS-CCD | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software package for the prediction of calpain cleavage sites. | calpain, cleavage detector, prediction | is listed by: OMICtools | PMID:21533053 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01673 | SCR_000202 | Calpain Cleavage Detector | 2026-02-14 01:59:39 | 4 | ||||||
|
Queensland Cyber Infrastructure Foundation Ltd Resource Report Resource Website |
Queensland Cyber Infrastructure Foundation Ltd (RRID:SCR_000208) | QCIF | nonprofit organization | Provides digital infrastructure capabilities for research and innovation across Queensland and Australia. Provides services, infrastructure and support for computation and data driven collaborative research and its application in industry. Members are six Queensland universities – The University of Queensland, Queensland University of Technology, Griffith University, James Cook University, CQUniversity, and the University of Southern Queensland. The University of the Sunshine Coast is an associate member. Member employees provide support and development services. | bioinformatics, contract, software, infrastructure, proteomics, metabolomics, clinical, dataset, analysis |
is listed by: ScienceExchange has parent organization: University of Queensland; Brisbane; Australia is parent organization of: QFAB Bioinformatics |
Queensland Government Department of Employment Economic Development and Innovation ; Commonwealth Government of Australia ; funded through its members |
Available to the research community in Australia | SciEx_4541 | http://www.scienceexchange.com/facilities/4541 | SCR_000208 | Queensland Parallel Supercomputing Foundation, qcif, the Queensland Cyber Infrastructure Foundation | 2026-02-14 01:59:39 | 0 | |||||
|
Multiple Myeloma Research Foundation Resource Report Resource Website 1+ mentions |
Multiple Myeloma Research Foundation (RRID:SCR_000207) | MMRF | institution | Research foundation that funds research to develop new treatments for multiple myeloma, an incurable blood cancer. | drug, treatment, cancer | is parent organization of: MMRF CoMMpass Study | Multiple myeloma | ISNI: 0000 0000 9350 5788, Crossref funder ID: 100001253, nlx_157895, Wikidata: Q6934894, grid.429426.f | https://ror.org/03ww1bx13 | SCR_000207 | 2026-02-14 01:59:39 | 9 | |||||||
|
Ohio Northern University; Ohio; USA Resource Report Resource Website |
Ohio Northern University; Ohio; USA (RRID:SCR_000362) | ONU | university | A public university in Ohio with land, sea and space grants that offers degree programs and research at the undergraduate and graduate level. | land, sea, space, grant, ohio, public | is parent organization of: Ohio Northern University College of Pharmacy | Wikidata:Q1683585, grid.261323.7, nlx_143792, ISNI:0000 0001 2187 1348 | https://ror.org/052963a64 | SCR_000362 | 2026-02-14 01:59:42 | 0 | ||||||||
|
riboPicker Resource Report Resource Website 1+ mentions |
riboPicker (RRID:SCR_000360) | software resource | Software to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets. | standalone software, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:22155869 | Free, Available for download, Freely available | OMICS_02618, biotools:ribopicker | https://bio.tools/ribopicker | SCR_000360 | 2026-02-14 01:59:42 | 2 | |||||||
|
ARACHNE Resource Report Resource Website 1+ mentions |
ARACHNE (RRID:SCR_000351) | ARACHNE | software resource | A software for genome assembly, and is specifically designed to analyze long Sanger-chemistry reads. | genome, sequencing, analysis, sanger, chemistry, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Broad Institute |
PMID:11779843 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01812, biotools:arachne | https://bio.tools/arachne | SCR_000351 | ARACHNE: a whole-genome shotgun assembler, ARACHNE (Unsupported) | 2026-02-14 01:59:42 | 3 | |||||
|
ParseCNV Resource Report Resource Website 1+ mentions |
ParseCNV (RRID:SCR_000355) | software resource | Software that takes CNV calls as input and creates SNP based statistics for CNV occurrence in cases and controls then calls CNVRs based on neighboring SNPs of similar significance. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23293001 | Free, Available for download, Freely available | OMICS_02566 | SCR_000355 | 2026-02-14 01:59:41 | 1 |
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