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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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RiceGE Resource Report Resource Website 50+ mentions |
RiceGE (RRID:SCR_015061) | data or information resource, database | Gene database for Japonica rice. RiceGE is associated with SIGnAL at the Salk Institute. | japonica rice, rice, gene, genome | has parent organization: SIGnAL Salk Institute Genomic Analysis Laboratory | Freely available | http://signal.salk.edu/cgi-bin/RiceGE5 | SCR_015061 | RiceGE: Genome Express Database, Rice Functional Genomic Express Database | 2026-09-05 06:32:11 | 87 | ||||||||
|
HumanBase Resource Report Resource Website 50+ mentions |
HumanBase (RRID:SCR_016145) | data or information resource, database | Formerly known as GIANT (Genome-scale Integrated Analysis of gene Networks in Tissues), HumanBase applies machine learning algorithms to learn biological associations from massive genomic data collections. These integrative analyses reach beyond existing "biological knowledge" represented in the literature to identify novel, data-driven associations. | genome, analysis, tissue, network, gene, machine, learning, biology | NCI T32 CA009528; NHGRI R01 HG005998; NHGRI T32 HG003284; NHLBI U54 HL117798; NIGMS P20 GM103534; NIGMS P50 GM071508; NIGMS R01 GM071966; US Department Of Health And Human Services HHSN272201000054C |
PMID:25915600 | Free, Public | SCR_016145 | GIANT (Genome-scale Integrated Analysis of gene Networks in Tissues), GIANT | 2026-09-05 06:32:13 | 95 | ||||||||
|
Genome Aggregation Database Resource Report Resource Website 5000+ mentions |
Genome Aggregation Database (RRID:SCR_014964) | gnomAD | data or information resource, database | Database that aggregates exome and genome sequencing data from large-scale sequencing projects. The gnomAD data set contains individuals sequenced using multiple exome capture methods and sequencing chemistries. Raw data from the projects have been reprocessed through the same pipeline, and jointly variant-called to increase consistency across projects. | database, genome, , bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: Broad Institute Genomics Platform has parent organization: Broad Institute has parent organization: Broad Institute of MIT and Harvard |
Broad Institute | Open source, Available to the biomedical community, The community can contribute to this resource | biotools:gnomad | https://github.com/macarthur-lab/gnomad_browser/issues, https://bio.tools/gnomad | SCR_014964 | gnomAD 2.0, gnomAD Browser, gnomAD version 2.0, Exome Aggregation Consortium | 2026-09-05 06:32:11 | 5310 | |||||
|
RegulomeDB Resource Report Resource Website 100+ mentions |
RegulomeDB (RRID:SCR_017905) | data or information resource, database, service resource | Database that annotates SNPs with known and predicted regulatory elements in intergenic regions of H. sapiens genome. Known and predicted regulatory DNA elements include regions of DNAase hypersensitivity, binding sites of transcription factors, and promoter regions that have been biochemically characterized to regulation transcription. Source of these data include public datasets from GEO, ENCODE project, and published literature. | Annotate, SNP, regulatory, DNA, element, intergenic, region, human, genome, sequence, DNAase, hypersensitivity, binding, site, transcription, factor, promoter, region, data, FASEB list | Beta Cell Consortium ; NHGRI U54 HG 004558 |
PMID:22955989 | Free, Freely available | SCR_017905 | 2026-09-05 06:32:15 | 161 | |||||||||
|
ABA Mouse Brain: Atlas Resource Report Resource Website 100+ mentions |
ABA Mouse Brain: Atlas (RRID:SCR_017479) | data or information resource, database, service resource | Genome wide database of gene expression in mouse brain. Genome-wide atlas of gene expression in the adult mouse brain. | Genome, data, gene, expression, mouse, brain |
has parent organization: Allen Institute for Brain Science is provided by: Allen Brain Atlas |
PMID:17151600 | Free, Freely available | SCR_017479 | Allen Brain Atlas: Mouse Brain, , Allen Brain Atlas Mouse Brain: Atlas | 2026-09-05 06:32:15 | 405 | ||||||||
|
Molecular Signatures Database Resource Report Resource Website 1000+ mentions |
Molecular Signatures Database (RRID:SCR_016863) | MSigDB | data or information resource, database | Collection of annotated gene sets for use with Gene Set Enrichment Analysis (GSEA) software. | collection, annotated, gene, set, GSEA, enrichment, analysis, genome, RNA, expression, data, FASEB list, DRKB |
uses: GSEA uses: Gene Set Enrichment Analysis has parent organization: Broad Institute |
NCI CA295532; NIGMS ; NIH |
Free, Freely available, Registration required to download GSEA software | https://www.gsea-msigdb.org/gsea/msigdb/ | SCR_016863 | Molecular Signatures Database, The Molecular Signatures Database, MSigDB, MSigDB database v6.2 | 2026-09-05 06:32:14 | 1702 | ||||||
|
GenomeScope Resource Report Resource Website 500+ mentions |
GenomeScope (RRID:SCR_017014) | Genomescope | data analysis software, data processing software, service resource, software application, software resource | Open source software package for fast genome analysis from unassembled short reads. Used to estimate genome heterozygosity, repeat content, and size from sequencing reads using a kmer-based statistical approach. | genome, unassembled, sequenced, data, short, read, analysis, heterozygosity, repeat, content, size, kmer | is related to: Cold Spring Harbor Laboratory | NHGRI R01 HG006677; NSF DBI 1350041; NSF IOS 1237880 |
PMID:28369201 | Free, Freely available, | http://qb.cshl.edu/genomescope/ | SCR_017014 | 2026-09-05 06:28:17 | 800 | ||||||
|
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 | 2026-09-05 06:28:17 | 1 | |||||||
|
shovill Resource Report Resource Website 500+ mentions |
shovill (RRID:SCR_017077) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool to assemble bacterial isolate genomes from Illumina paired end reads. Used for isolate data only, primarily small haploid organisms. Supports assemblers like SKESA, Velvet and Megahit. | assembly, bacteria, isolate, genome, Illumina, paired, end, read, data, haploid, organism, bio.tools |
uses: SPAdes is listed by: Debian is listed by: bio.tools is related to: Trimmomatic is related to: SAMTOOLS is related to: BWA is related to: FLASH is related to: Velvet is related to: Pilon |
Free, Available for download, Freely available | , biotools:shovill, BioTools:shovill | https://bio.tools/shovill, https://sources.debian.org/src/shovill/ | SCR_017077 | 2026-09-05 06:28:18 | 587 | ||||||||
|
VAPPER Resource Report Resource Website 1+ mentions |
VAPPER (RRID:SCR_016993) | VAPPER | data analysis software, data processing software, software application, software resource | Software tool for analysis of variant antigens in African trypanosomes. Used for quantitative analysis of antigenic diversity in systems data of genomes, transcriptomes, and proteomes, called Variant Antigen Profiling to understand how antigenic diversity relates to clinical outcome, how antigen genes may be used as epidemiological markers of virulence, and in measuring gene expression during experimental infections. | variant, antigen, profiling, data, genome, transcriptome, proteome, gene, expression, infection, Trypanosoma, bio.tools |
is listed by: Debian is listed by: bio.tools requires: Python Programming Language |
Free, Available for download, Freely available | biotools:VAPPER | https://bio.tools/VAPPER | SCR_016993 | VAP, VariantAntigenProfilingPER | 2026-09-05 06:28:16 | 1 | ||||||
|
rnaSPAdes Resource Report Resource Website 50+ mentions |
rnaSPAdes (RRID:SCR_016992) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for assembling transcripts from RNA-Seq data. Explores surprising computational parallels between assembly of transcriptomes and single cell genomes. Suitable for all kind of organisms. Part of SPAdes package since version 3.9. | assembling, transcript, RNA-Seq, data, single, cell, genome, analysis, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: SPAdes is related to: rnaQUAST |
Russian Science Foundation 14-50-00069 | DOI:10.1101/420208 | Free, Available for download, Freely available | biotools:rnaSPAdes_autogenerated | https://bio.tools/rnaSPAdes_autogenerated | SCR_016992 | 2026-09-05 06:28:16 | 58 | ||||||
|
Goseq Resource Report Resource Website 100+ mentions |
Goseq (RRID:SCR_017052) | data analysis software, data processing software, software application, software resource | Software application for performing Gene Ontology analysis on RNAseq data and other length biased data. Used to reduce complexity and highlight biological processes in genome wide expression studies. | Gene, Ontology, analysis, RNAseq, data, sequencing, genome, expression, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
PMID:20132535 | Free, Available for download, Freely available | biotools:goseq | https://bio.tools/goseq | SCR_017052 | 2026-09-05 06:28:17 | 382 | |||||||
|
CPTAC Resource Report Resource Website 100+ mentions |
CPTAC (RRID:SCR_017135) | consortium, data or information resource, disease-related portal, organization portal, portal, topical portal | Clinical proteomic tumor analysis consortium to systematically identify proteins that derive from alterations in cancer genomes and related biological processes, in order to understand molecular basis of cancer that is not possible through genomics and to accelerate translation of molecular findings into clinic. Operates through Proteome Characterization Centers, Proteogenomic Translational Research Centers, and Proteogenomic Data Analysis Centers. CPTAC investigators collaborate, share data and expertise across consortium, and participate in consortium activities like developing standardized workflows for reproducible studies. | identify, protein, alteration, cancer, genome, clinical, study, proteome, proteogenomic, tumor, data, analysis, consortium, reproducibility | has parent organization: National Cancer Institute | cancer | SCR_017135 | Clinical Proteomic Tumor Analysis Consortium | 2026-09-05 06:28:19 | 213 | |||||||||
|
University of Cambridge Centre for Trophoblast Research Bioinformatics Core Facility Resource Report Resource Website |
University of Cambridge Centre for Trophoblast Research Bioinformatics Core Facility (RRID:SCR_017192) | CTR Bioinformatics Core Facility | access service resource, analysis service resource, core facility, data analysis service, production service resource, service resource, training service resource | Core provides assistance with experimental design, RNA sequencing, whole genome and targeted sequencing, methylation sequencing, protein alignment, microscopy image analysis, and training. | bioinformatics, sequencing, RNA, genome, methylation, protein, alignment, data, image, analysis | has parent organization: University of Cambridge; Cambridge; United Kingdom | Restricted | SCR_017192 | Center for Trophoblast Research, Centre for Trophoblast Research, Bioinformatics Core Facility, University of Cambridge | 2026-09-05 06:28:20 | 0 | ||||||||
|
miRquant Resource Report Resource Website 1+ mentions |
miRquant (RRID:SCR_017261) | data analysis software, data analytics software, data processing software, software application, software resource | Software tool for accurate annotation and quantification of microRNAs and their isomiRs from small RNA-sequencing data. Provides information on quality of sequencing data, genome mapping statistics, abundance of other types of small RNAs such as tDRs and yDRs, prevalence of post transcriptional modifications. | annotation, quantification, miRNA, smRNA-seq, data, functionally, distinct, isoform, isomiR, quality, sequencing, genome, mapping, statistic, tDR, yDR | PMID:28187421 | Free, Available for download, Freely available | SCR_017261 | miRquant 2.0 | 2026-09-05 06:28:21 | 1 | |||||||||
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PathwayNet Resource Report Resource Website 1+ mentions |
PathwayNet (RRID:SCR_017353) | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks. | Interface, interaction, predict, human, gene, network, integrative, analysis, user, data, tissue, cell, functional, protein, genome |
is listed by: OMICtools has parent organization: Princeton University; New Jersey; USA |
NHGRI HG005998; NIGMS P50 GM071508; NIGMS R01 GM071966 |
PMID:25431329 | Free, Freely available | SCR_017353 | 2026-09-05 06:28:23 | 8 | ||||||||
|
peddy Resource Report Resource Website 10+ mentions |
peddy (RRID:SCR_017287) | data analysis software, data analytics software, data processing software, software application, software resource | Software package that evaluates correspondence between stated sexes, relationships, and ancestries in pedigree file and those inferred from genotypes in VCF file resulting from human whole genome sequencing or whole exome sequencing studies. Facilitates both automated and interactive, visual detection of sample swaps, poor sequencing quality, and other indicators of sample problems. | sex, relation, ancestry, evaluate, pedigree, VCF file, genome, sequencing, exome, error, genotype | has parent organization: University of Utah; Utah; USA | NHGRI R01 HG006693 | PMID:28190455 | Free, Available for download, Freely available | http://quinlanlab.org/#portfolioModal8 | SCR_017287 | 2026-09-05 06:28:22 | 10 | |||||||
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NOVOPlasty Resource Report Resource Website 100+ mentions |
NOVOPlasty (RRID:SCR_017335) | alignment software, data processing software, image analysis software, software application, software resource | Software package as de novo assembler and heteroplasmy variance caller for short circular genomes. Used for de novo assembly of organelle genomes from whole genome data. | de novo, assembler, heteroplasmy, variance, caller, short, circular, genome, organelle, whole, data | is listed by: OMICtools | Belgian Kids Fund ; Hôpital Universitaire des Enfants Reine Fabiola ; Interuniversity Institute of Bioinformatics in Brussels |
PMID:28204566 | Free, Available for download, Freely available | SCR_017335 | 2026-09-05 06:28:23 | 202 | ||||||||
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Computing Genome Assembly Likelihoods Resource Report Resource Website 100+ mentions |
Computing Genome Assembly Likelihoods (RRID:SCR_017624) | CGAL | alignment software, data processing software, image analysis software, software application, software resource | Software tool for computing genome assembly likelihoods.Computes likelihood of reads with respect to assembly and statistical model which can be used as metric for evaluating assemblies. Novel likelihood based approach to assembly assessment in absence of ground truth. | Computing, genome, assembly, likelihood, read, evaluation | Fulbright Science & Technology Fellowship ; NHGRI R21 HG006583 |
PMID:23360652 | http://bio.math.berkeley.edu/cgal/ | SCR_017624 | 2026-09-05 06:28:27 | 106 | ||||||||
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Batch Data and Analysis Tool Resource Report Resource Website 1+ mentions |
Batch Data and Analysis Tool (RRID:SCR_017515) | data or information resource, service resource | Software tool to access various mouse genome information in batch format. Batch data and analysis tools. | Mouse, genome, information, batch, format, data, analysis, tool | has parent organization: Mouse Genome Informatics (MGI) | Free, Freely available | SCR_017515 | 2026-09-05 06:28:25 | 3 |
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