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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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TASSEL Resource Report Resource Website 1000+ mentions |
TASSEL (RRID:SCR_012837) | TASSEL | software application, software resource | Software package which performs a variety of genetic analyses including association mapping, diversity estimation and calculating linkage disequilibrium. The association analysis between genotypes and phenotypes can be performed by either a general linear model or a mixed linear model. The general linear model now allows users to analyze complex field designs, environmental interactions, and epistatic interactions. The mixed model is specially designed to handle polygenic effects at multiple levels of relatedness including pedigree information. These new analyses should permit association analysis in a wide range plant and animal species. (entry from Genetic Analysis Software) | gene, genetic, genomic, java, web-based, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
nlx_154674, biotools:tassel | http://sourceforge.net/projects/tassel/, https://bio.tools/tassel | SCR_012837 | and Linkage, Trait Analysis by aSSociation, Evolution | 2026-09-12 01:02:48 | 2476 | |||||||
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MCLEEPS Resource Report Resource Website |
MCLEEPS (RRID:SCR_013062) | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, unix, macos | is listed by: Genetic Analysis Software | nlx_154469 | SCR_013062 | Monte Carlo Likelihood Estimation of Effective Population Size PANGAEA | 2026-09-12 01:02:48 | 0 | |||||||||
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UTIL Resource Report Resource Website 1+ mentions |
UTIL (RRID:SCR_009424) | UTIL | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, pascal, ms-windows, linux | is listed by: Genetic Analysis Software | PMID:23546798 | nlx_154685 | SCR_009424 | statistical genetics UTILity programs | 2026-09-12 01:02:46 | 2 | |||||||
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TREESELECT Resource Report Resource Website 1+ mentions |
TREESELECT (RRID:SCR_009422) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 6th,2023. Software package for inferring natural selection from unusual population differentiation between closely related populations. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154682 | SCR_009422 | 2026-09-12 01:02:46 | 4 | |||||||||
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DETONATE Resource Report Resource Website 1+ mentions |
DETONATE (RRID:SCR_017035) | DETONATE | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool to evaluate de novo transcriptome assemblies from RNA-Seq data. Consists of RSEM-EVAL and REF-EVAL packages. RSEM-EVAL is reference-free evaluation method. REF-EVAL is reference based and can be used to compare sets of any kinds of genomic sequences. | evaluate, de novo, transcriptome, assembly, RNAseq, data, RSEM-EVAL, REF-EVAL, dataset, genomic, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
NHGRI R01 HG005232; NLM T15 LM007359 |
PMID:25608678 | Free, Available for download, Freely available | biotools:detonate | https://bio.tools/detonate | SCR_017035 | DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation, DETONATE | 2026-09-12 01:00:19 | 2 | ||||
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Illumina: HiSeq 1500 System Resource Report Resource Website 1+ mentions |
Illumina: HiSeq 1500 System (RRID:SCR_018006) | instrument resource | High-throughput sequencing system. Support of instrument and supply reagents will be provided through February 28th, 2023. Other instruments that support same applications as HiSeq 1500 System are available. Use Sequencing Platform Comparison Tool to find the best instrument for your needs. | Illumina, genomic, hardware, instrument, equipment, sequencer, sequencing | Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_018006.pdf | https://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/hiseq1500/hiseq-1500-system-guide-15035788-03.pdf | SCR_018006 | HiSeq 1500 System | 2026-09-12 12:58:56 | 1 | ||||||||
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CoronaVIR Resource Report Resource Website 1+ mentions |
CoronaVIR (RRID:SCR_018338) | data or information resource, disease-related portal, portal, topical portal | Web based platform on COVID-19 to maintain predicted diagnostic, drug and vaccine candidates and computational resources on novel coronavirus SARS-CoV-2 and its resulting disease COVID-19. Provides collected and organized information from literature and other resources from internet, links to appropriate literature . Integrated multi-omics repository dedicated to current genomic, proteomic, diagnostic and therapeutic knowledge about coronaviruses. | COVID-19, SARS-CoV-2, diagnostic, drug, candidate, computational resource. coronavirus, disease, literature, genomic, proteomic, data | COVID-19 | DOI:10.31219/osf.io/xegzu | Free, Freely available | SCR_018351 | SCR_018338 | 2026-09-12 12:59:00 | 4 | ||||||||
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Blixem Resource Report Resource Website 1+ mentions |
Blixem (RRID:SCR_015994) | alignment software, data processing software, image analysis software, software application, software resource | Software for sequence alignments that displays multiple match sequences aligned against a single genomic reference sequence. It can be used for manipulation, display and annotation of genomic data, to check the quality of an alignment, to find missing/misaligned sequence, and to identify splice sites and polyA sites. | software, sequence, alignment, annotation, genomic, reference, data, display, manipulation, DNA |
is related to: SEQtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
NHGRI U54 HG00455; Wellcome Trust Grant 098051 |
PMID:26801397 | Free, Available for download | SCR_015994 | SEQtools Blixem | 2026-09-12 12:58:34 | 2 | |||||||
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Allen Brain Atlas Resource Report Resource Website 100+ mentions |
Allen Brain Atlas (RRID:SCR_017001) | atlas, data or information resource, portal, project portal | Portal provides access to data and web based applications created for benefit of global research community by Allen Institute for Brain Science. Projects to ombine genomics with neuroanatomy by creating gene expression maps for mouse and human brain. Mouse Brain Atlas, Human Brain Atlas, Developing Mouse Brain Atlas, Developing Human Brain Atlas, Mouse Connectivity Atlas, Non-Human Primate Atlas, and Mouse Spinal Cord Atlas and three related projects Glioblastoma, Mouse Diversity, and Sleep data banks, are used to advance various fields of science especially in neurobiological diseases. | genomic, data, neuroanatomy, gene, expression, map, mouse, human, brain, atlas, neurobiology |
is related to: Allen Software Development Kit is related to: Common Cell Type Nomenclature has parent organization: Allen Institute has parent organization: Allen Institute for Brain Science is parent organization of: Allen Mouse Brain Reference Atlas is parent organization of: Allen Human Brain Atlas is parent organization of: Allen Developing Mouse Brain Atlas is parent organization of: Allen Mouse Brain Connectivity Atlas is parent organization of: Allen Mouse Spinal Cord Atlas is parent organization of: CellTax vignette is parent organization of: Allen Brain Atlas expression map of Cre and other drivers provides: ABA Mouse Brain: Atlas works with: Transcriptomics Explorer works with: Kinase Associated Neural Phospho Signaling |
Free, Freely available | SCR_017530 | SCR_017001 | Allen Brain Atlas, Brain Atlases, Allen Mouse Brain Atlas, The Allen Brain Atlas, Allen Human Brain Atlas | 2026-09-12 12:58:47 | 237 | ||||||||
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OmicsSIMLA Resource Report Resource Website 1+ mentions |
OmicsSIMLA (RRID:SCR_017011) | simulation software, software application, software resource, software toolkit | Software tool for generating multi omics data with disease status. Simulates genomics (SNPs and copy number variations), epigenomics ( whole genome bisulphite sequencing), transcriptomics ( RNA seq), and proteomics (normalized reverse phase protein array) data at the whole genome level. Available as desktop and web application version. | multi, omics, data, simulator, disease, genomic, epigenomic, transcriptomic, proteomic, genome, sequencing, protein, RNA | is listed by: OMICtools | Ministry of Science and Technology in Taiwan | DOI:10.1101/426510 | Freely available, Available to download, Free | OMICS_31363 | SCR_017011 | 2026-09-12 12:58:47 | 1 | |||||||
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Italian Institute for Genomic Medicine; Turin; Italy Resource Report Resource Website |
Italian Institute for Genomic Medicine; Turin; Italy (RRID:SCR_017062) | IIGM, HuGeF | data or information resource, portal, topical portal | Private research institute in Turin, Italy. Research programs in immunogenetics, functional genomics, genomic epidemiology, tumour diagnostic and prognostic biomarker research, epigenetic modifications in disease, quantitative biology and computational neuroscience. | institute, private, research, human, genetic, genomic, epigenomic, immunogenetic, quantitative, biology, computational, neuroscience | is parent organization of: HaTSPiL | SCR_017062 | 2026-09-12 12:58:48 | 0 | ||||||||||
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Genomic Ranges Resource Report Resource Website 1+ mentions |
Genomic Ranges (RRID:SCR_017051) | data analysis software, data processing software, software application, software resource, software toolkit | Software R package for computing and annotating genomic ranges. Used for storing and manipulating genomic intervals and variables defined along genome. | computing, annotating, genomic, range, storing, manipulating, interval, variable, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
NHGRI P41 HG004059; NHGRI U41 HG004059; NHLBI R01 HL086601; NHLBI R01 HL093076; NHLBI R01 HL094635 |
PMID:23950696 | Free, Available for download, Freely available | biotools:genomicranges | https://bio.tools/genomicranges | SCR_017051 | 2026-09-12 12:58:47 | 2 | ||||||
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Nuclear Hormone Receptor Scan Resource Report Resource Website 1+ mentions |
Nuclear Hormone Receptor Scan (RRID:SCR_016975) | NHR-scan | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web interface for computational prediction of nuclear hormone receptor binding sites in genomic sequences. Flexible Hidden Markov Model framework to allow for variable spacing and orientation of half sites. Allows for parameter modifications. | prediction, nuclear, hormone, receptor, binding, site, genomic, sequence, parameter, modification, analysis | is listed by: OMICtools | Canadian Institutes of Health Research ; Pharmacia Corporation to the Center for Genomics and Bioinformatics |
PMID:15563547 | Free, Available, Acknowledgement requested | OMICS_14042 | SCR_016975 | NHR-scan, NHR Scan, NHRScan, Nuclear Hormoe Receptor Scan | 2026-09-12 12:58:46 | 5 | |||||
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Genome Institute of Singapore Scientific and Research Computing Core Facility Resource Report Resource Website |
Genome Institute of Singapore Scientific and Research Computing Core Facility (RRID:SCR_017193) | GIS Scientific and Research Computing | access service resource, analysis service resource, core facility, data analysis service, production service resource, service resource, software resource | Core provides research computing resources including bioinformatics, application development, data management and IT infrastructure to support next generation sequencing technologies, human genotyping, high throughput screening and computational biology researchers. | bioinformatics, genomic, data, management, next, generation, sequencing, genotyping, analysis | Open | SCR_017193 | Core Facility, GIS, Scientific & Research Computing, Scientific and Research Computing, Genome Institute of Singapore | 2026-09-12 12:58:49 | 0 | |||||||||
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Montreal Clinical Research Bioinformatics Core Facility Resource Report Resource Website |
Montreal Clinical Research Bioinformatics Core Facility (RRID:SCR_017176) | IRCM BIF, BIF | access service resource, analysis service resource, core facility, data analysis service, data or information resource, production service resource, service resource, training service resource | Core to support scientists within and outside IRCM in analysis of biological and clinical data, in particular high throughput genomic data. Operating on collaborative basis and paid services. Provides assistance with Data analysis for RNA-Seq, ChIP-Seq, RIP-Seq, DNA methylation, DNA-Seq, targeted sequencing of rRNAs, microarrays, customized training courses. | bioinformatics, genomic, omics, data, analysis, RNA-Seq, CHIP-Seq, RIP-Seq, DNA, methylation, DNA-Seq, rRNA, microarray | Restricted | SCR_017176 | , Institute of Clinical Research of Montreal, IRCM, Bioinformatics Core Facility, BIF | 2026-09-12 12:58:49 | 0 | |||||||||
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RepeatFiller Resource Report Resource Website 10+ mentions |
RepeatFiller (RRID:SCR_017414) | alignment software, data processing software, image analysis software, software application, software resource | Software tool to incorporate newly detected repeat overlapping alignments into pairwise alignment chains. It only aligns local genomic regions that are bounded by colinear aligning blocks, as provided in chains, which makes it feasible to consider all seeds including those that overlap repetitive regions. Used to improve genome alignments by incorporating previously undetected local alignments between repetitive sequences. | Repeat, overlapping, alignment, pairwise, chain, local, genomic, region, colinear, block, sequence, undetected, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Max Planck Institute of Molecular Cell Biology and Genetics; Dresden; Germany |
DOI:10.1101/696922 | Free, Freely available | biotools:RepeatFiller, BioTools:RepeatFiller | https://bio.tools/RepeatFiller, https://bio.tools/RepeatFiller, https://bio.tools/RepeatFiller | SCR_017414 | 2026-09-12 12:58:52 | 16 | |||||||
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GCE Resource Report Resource Website 10+ mentions |
GCE (RRID:SCR_017332) | data analysis software, data processing software, software application, software resource | Software tool for estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects. Used as general and assembly independent method for estimating genomic characteristics. | estimation, genomic, characteristic, analysis, k-mer, frequencey, de novo | ftp://ftp.genomics.org.cn/pub/gce | SCR_017332 | Genomic Characteristics Estimation | 2026-09-12 12:58:51 | 15 | ||||||||||
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4D Genome Resource Report Resource Website 10+ mentions |
4D Genome (RRID:SCR_017489) | data or information resource, data repository, database, service resource, storage service resource | Repository for chromatin interaction data. Records can be queried by genomic regions, gene names, organism, and detection technology. Database is continuously updated by curators. Contributions from scientific community. | Repository, chromatic, interaction, data, genomic, region, gene, name, detection, technology, curated | has parent organization: University of Pennsylvania; Philadelphia; USA | Free, Available for download, Freely available | r3d100012282 | https://doi.org/10.17616/R3SH37 | SCR_017489 | 2026-09-12 12:58:53 | 11 | ||||||||
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AmoebaDB Resource Report Resource Website 1+ mentions |
AmoebaDB (RRID:SCR_017592) | analysis service resource, data or information resource, database, production service resource, service resource | Integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. Contains genomes of three Entamoeba species and microarray expression data for E. histolytica. Integrates whole genome sequence and annotation and includes experimental data and environmental isolate sequences provided by community researchers. | Genomic, functional, database, Entamoeba, Acanthamoeba, parasite, microarray, expression, data, experimental, isolate, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Eukaryotic Pathogen Database Resources |
Department of Health and Human Services ; NIDA ; NIH |
PMID:20974635 | Free, Freely available | biotools:amoebadb, r3d100012457 | https://bio.tools/amoebadb, https://doi.org/10.17616/R3PX9Q | SCR_017592 | 2026-09-12 12:58:54 | 8 | ||||||
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Starbase V2.0 Resource Report Resource Website 1000+ mentions |
Starbase V2.0 (RRID:SCR_016303) | software resource, web application | Web based tool to visualize, analyze, discover and download of large-scale functional genomics data. Used for analysis of the CLIP-Seq and Degradome-Seq data sets, exploration of miRNA–target interactions and decoding RNA interaction networks from CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) data. To show RNA-RNA and protein-RNA interaction networks in developmental, physiological and pathological processes. | visualize, analyze, discover, download, large, genomic, data, set, miRNA, RNA-RNA, protein-RNA, interaction, network, decoding, CLIP-Seq, Degradome-Seq | Ministry of Science and Technology of China ; National Basic Research Program No. 2011CB811300 |
PMID:24297251 | Free, Freely available, Available for download | SCR_016303 | 2026-09-12 12:58:37 | 1004 |
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