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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CHASM/SNV-Box Resource Report Resource Website 1+ mentions |
CHASM/SNV-Box (RRID:SCR_006445) | CHASM/SNV-Box | data or information resource, database, software resource | CHASM is a method that predicts the functional significance of somatic missense mutations observed in the genomes of cancer cells, allowing mutations to be prioritized in subsequent functional studies, based on the probability that they give the cells a selective survival advantage. SNV-Box is a database of pre-computed features of all possible amino acid substitutions at every position of the annotated human exome. Users can rapidly retrieve features for a given protein amino acid substitution for use in machine learning. | is listed by: OMICtools | Cancer | NCI CA152432; NCI CA135866; NSF DBI0845275 |
Acknowledgement requested, Free, Non-commercial | OMICS_00127 | SCR_006445 | CHASM / SNV-Box, Cancer-specific High-throughput Annotation of Somatic Mutations | 2026-09-19 12:51:11 | 3 | ||||||
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FlyBase Resource Report Resource Website 1000+ mentions |
FlyBase (RRID:SCR_006549) | FB | data or information resource, data repository, database, organism-related portal, portal, service resource, storage service resource, topical portal | Database of Drosophila genetic and genomic information with information about stock collections and fly genetic tools. Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular function, the biological processes in which they play a role, and their subcellular location. Additionally, FlyBase accepts data submissions. FlyBase can be searched for genes, alleles, aberrations and other genetic objects, phenotypes, sequences, stocks, images and movies, controlled terms, and Drosophila researchers using the tools available from the "Tools" drop-down menu in the Navigation bar. | RIN, Resource Information Network, mutant, gene, genome, blast, genotype, phenotype, allele, sequence, stock, image, movie, controlled term, video resource, image collection, life-cycle, genome, expression, rna-seq, genetics, drosophilidae, bio.tools, FASEB list, RRID Community Authority |
is used by: NIF Data Federation is used by: Resource Identification Portal is used by: PhenoGO is used by: Integrated Animals is used by: Drososhare is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: Resource Information Network is related to: FlyMine is related to: Virtual Fly Brain is related to: AmiGO is related to: Drosophila melanogaster Exon Database is related to: HomoloGene is related to: UniParc at the EBI is related to: UniParc is related to: Gene Ontology is related to: NIH Data Sharing Repositories is related to: GBrowse is related to: Integrated Manually Extracted Annotation is related to: PhenoGO has parent organization: Harvard University; Cambridge; United States has parent organization: University of Cambridge; Cambridge; United Kingdom has parent organization: Indiana University; Indiana; USA has parent organization: University of New Mexico; New Mexico; USA is parent organization of: Drosophila anatomy and development ontologies is parent organization of: Fly Taxonomy is parent organization of: FlyBase Controlled Vocabulary is parent organization of: Drosophila Development Ontology is organization facet of: Alliance of Genome Resources |
Indiana Genomics Initiative ; MRC ; NIH Blueprint for Neuroscience Research ; NIHGRI P41 HG000739; NSF |
PMID:24234449 PMID:22127867 PMID:18948289 PMID:18641940 PMID:18160408 PMID:17099233 PMID:16381917 PMID:15608223 PMID:12519974 PMID:11752267 PMID:11465064 PMID:9847148 PMID:9399806 PMID:9045212 PMID:8594600 PMID:8578603 PMID:7937045 PMID:7925011 |
nif-0000-00558, r3d100010591, OMICS_01649, biotools:flybase | https://bio.tools/flybase, https://doi.org/10.17616/R3903Q | http://flybase.net | SCR_006549 | flybase A Drosophila Genomic and Genetic Database, FlyBase: A Database of Drosophila Genes and Genomes, FLYBASE, FlyBase: A Database of Drosophila Genes & Genomes, FB | 2026-09-19 12:51:13 | 4234 | ||||
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Decombinator Resource Report Resource Website 10+ mentions |
Decombinator (RRID:SCR_006732) | data analysis software, data processing software, software application, software resource, software toolkit | Software suite for analysis of T cell receptor repertoire data. Used for fast, efficient analysis of T cell receptor (TcR) repertoire samples, designed to be accessible to those with no previous programming experience. | Python, t-cell receptor sequence, t-cell receptor, sequence, deep sequencing, TCR repertoires, repertoire data, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University College London; London; United Kingdom |
PMID:23303508 PMID:32853330 |
Free, Available for download, Freely available | biotools:decombinator, OMICS_00001 | https://github.com/innate2adaptive/Decombinator, https://bio.tools/decombinator | SCR_006732 | Decombinator v2.2, Decombinator v4.0.3 | 2026-09-19 12:51:17 | 32 | ||||||
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FDM Resource Report Resource Website 1+ mentions |
FDM (RRID:SCR_006733) | FDM | software resource | A graph-based statistical method to detect differential transcription using RNA-seq data. | is listed by: OMICtools | OMICS_01332 | SCR_006733 | 2026-09-19 12:51:17 | 1 | ||||||||||
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htSeqTools Resource Report Resource Website 10+ mentions |
htSeqTools (RRID:SCR_006614) | htSeqTools | software resource | Software tools for quality control, visualization and processing for High-Throughput Sequencing data. These include MDS plots (analogues to PCA), detecting inefficient immuno-precipitation or over-amplification artifacts, tools to identify and test for genomic regions with large accumulation of reads, and visualization of coverage profiles. | high-throughput sequencing, chip-seq, rnaseq |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_01233 | SCR_006614 | 2026-09-19 12:51:14 | 11 | |||||||||
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InterPro Resource Report Resource Website 5000+ mentions |
InterPro (RRID:SCR_006695) | InterPro | analysis service resource, data access protocol, data analysis service, data or information resource, database, production service resource, service resource, software resource, web service | Service providing functional analysis of proteins by classifying them into families and predicting domains and important sites. They combine protein signatures from a number of member databases into a single searchable resource, capitalizing on their individual strengths to produce a powerful integrated database and diagnostic tool. This integrated database of predictive protein signatures is used for the classification and automatic annotation of proteins and genomes. InterPro classifies sequences at superfamily, family and subfamily levels, predicting the occurrence of functional domains, repeats and important sites. InterPro adds in-depth annotation, including GO terms, to the protein signatures. You can access the data programmatically, via Web Services. The member databases use a number of approaches: # ProDom: provider of sequence-clusters built from UniProtKB using PSI-BLAST. # PROSITE patterns: provider of simple regular expressions. # PROSITE and HAMAP profiles: provide sequence matrices. # PRINTS provider of fingerprints, which are groups of aligned, un-weighted Position Specific Sequence Matrices (PSSMs). # PANTHER, PIRSF, Pfam, SMART, TIGRFAMs, Gene3D and SUPERFAMILY: are providers of hidden Markov models (HMMs). Your contributions are welcome. You are encouraged to use the ''''Add your annotation'''' button on InterPro entry pages to suggest updated or improved annotation for individual InterPro entries. | protein, classify, prediction, protein domain, genome, protein family, functional site, protein sequence, protein function, analysis, nucleic acid, amino acid, amino acid sequence, gold standard |
is listed by: re3data.org is listed by: OMICtools is related to: TIGRFAMS is related to: TIGRFAMS is related to: FlyMine is related to: GeneSpeed- A Database of Unigene Domain Organization is related to: Biomine is related to: InterProScan is related to: GeneTerm Linker is related to: Gene Ontology is related to: ProDom is related to: Algal Functional Annotation Tool has parent organization: European Bioinformatics Institute |
European Union FP7 Scientific Data Repositories 213037; BBSRC BB/F010508/1; NIGMS GM081084 |
PMID:22096229 PMID:21082426 PMID:18940856 PMID:18428686 PMID:18025686 PMID:17202162 PMID:16909843 PMID:15608177 PMID:12520011 PMID:12230031 PMID:11159333 PMID:11119311 PMID:11125043 |
Acknowledgement requested, Free, Public, The community can contribute to this resource | nif-0000-03035, OMICS_01694, r3d100010798 | https://doi.org/10.17616/R3FS61 | SCR_006695 | InterPro: protein sequence analysis & classification, InterPro protein sequence analysis and classification | 2026-09-19 12:51:16 | 7722 | ||||
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SToRM Resource Report Resource Website 100+ mentions |
SToRM (RRID:SCR_006696) | SToRM | software resource | A software tool primarily proposed for mapping SOLiD reads or Illumina reads to a reference genome. It was based on seeding techniques adapted to the statistical characteristics of the reads: the default seeds are for example designed (using the Iedera software) to comply with the properties of the SOLiD color encoding, or Illumina more classical encoding as well as the observed reading error distribution along the read., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | c, linux, macos, solid |
is listed by: OMICtools has parent organization: University Lille 1 - Sciences and Technologies; Lille; France |
PMID:20936175 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00692 | SCR_006696 | 2026-09-19 12:51:16 | 205 | |||||||
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GARM Resource Report Resource Website 10+ mentions |
GARM (RRID:SCR_006731) | GARM | software resource | A new software pipeline to merge and reconcile assemblies from different algorithms or sequencing technologies. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01420 | SCR_006731 | Genome Assembler Reconcilation and Merging | 2026-09-19 12:51:17 | 12 | |||||||||
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DGIdb Resource Report Resource Website 100+ mentions |
DGIdb (RRID:SCR_006608) | DGIdb | application programming interface, data access protocol, data or information resource, database, software resource | A database of drug-gene relationships that provides drug-gene interactions and potential druggability data given list of genes. There are about 15 data sources that are being aggregated by DGIdb, with update date and these data sources are listed on this page: http://dgidb.genome.wustl.edu/sources, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | drug, gene, interaction, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Washington University in St. Louis; Missouri; USA |
Cancer | NHGRI U54 HG003079 | PMID:24122041 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155686, biotools:DGIdb, OMICS_01579 | https://bio.tools/DGIdb | SCR_006608 | Drug-Gene Interaction database, Drug Gene Interaction Database | 2026-09-19 12:51:14 | 408 | |||
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PROGENY Resource Report Resource Website 100+ mentions |
PROGENY (RRID:SCR_006647) | Progeny | commercial organization, data management software, software application, software resource | Fully customizable, comprehensive genetic pedigree and clinical data management software including a multi-user relational database with an integrated pedigree drawing component to manage genetic and pedigree data in one database. Manage Pedigrees, Individuals, SNPs, STRs, Samples, Plates, Genotypes and exports to multiple analysis platforms. (entry from Genetic Analysis Software) * LIMS software, providing advanced sample tracking and management (including functionality to generate and record barcodes) and configurable workflows for your specific environment. * Full genotype management gives users the ability to track not only family-based studies, but Whole Genome Association studies containing 1000''s of samples with large arrays. | gene, genetic, genomic, c++, active x control, ms-windows, pedigree, clinical, genotype, data management, drawing, family history, questionnaire, sample, lab management, FASEB list |
is listed by: OMICtools is listed by: Genetic Analysis Software |
nlx_154553, OMICS_00216 | SCR_006647 | Progeny Software LLC, Progeny Software | 2026-09-19 12:51:15 | 416 | ||||||||
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FLUX CAPACITOR Resource Report Resource Website 1+ mentions |
FLUX CAPACITOR (RRID:SCR_006651) | FLUX CAPACITOR | software resource | Software to recontruct abundances of known transcript forms from RNAseq data. The algorithm works by distributing the reads mapping to a given exonic region (or splice junction) among the transcripts including the exon (or splice junction). The input is the annotation of a reference transcriptome and reads from RNAseq technologies aligned to the genome. From the reference annotation, splicing graphs are produced and reads are mapped to corresponding edges in these graphs according to the position where they align in the genomic sequence. The resulting graph with edges labelled by the number of reads can be interpreted as a flow network where each transcript representing a transportation path from its start to its end and consequently each edge a possibly shared segment of transportation along which a certain number of reads per nucleotide -- i.e., a flux -- is observed. Given a density function of reads along a transcript, the expected participation of each transcript in an edge under consideration can be estimated. The basic idea is to cast back from these latter participations and the observed number of reads - allowing for a certain amount of noise - to the original transcript abundancies. To do so, a linear constraint is formalized for each edge, and an optimal solution for the complete set of constraints is found by a standard linear program solver. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:20220756 | biotools:the_flux_capacitor, OMICS_01293 | https://bio.tools/the_flux_capacitor | SCR_006651 | The FLUX CAPACITOR, FluxCapacitor | 2026-09-19 12:51:15 | 2 | ||||||
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TIGAR Resource Report Resource Website 10+ mentions |
TIGAR (RRID:SCR_006650) | TIGAR | software resource | Software to estimate transcript isoform abundances from RNA-Seq data by variational Bayesian inference. The statistical method can handle gapped alignments of reads against reference sequences so that it allows insertion or deletion errors within reads. | is listed by: OMICtools | PMID:23821651 | OMICS_01294 | SCR_006650 | TIGAR: Transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference | 2026-09-19 12:51:15 | 46 | ||||||||
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APOLLOH Resource Report Resource Website 10+ mentions |
APOLLOH (RRID:SCR_006648) | APOLLOH | software resource | A hidden Markov model (HMM) for predicting somatic loss of heterozygosity and allelic imbalance in whole tumour genome sequencing data. |
is listed by: OMICtools has parent organization: BC Cancer Agency |
OMICS_00306 | SCR_006648 | 2026-09-19 12:51:15 | 21 | ||||||||||
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MaizeGDB Resource Report Resource Website 1000+ mentions |
MaizeGDB (RRID:SCR_006600) | MaizeGDB | analysis service resource, data analysis service, data or information resource, data repository, database, organism-related portal, portal, production service resource, service resource, storage service resource, topical portal | Collection of data related to crop plant and model organism Zea mays. Used to synthesize, display, and provide access to maize genomics and genetics data, prioritizing mutant and phenotype data and tools, structural and genetic map sets, and gene models and to provide support services to the community of maize researchers. Data stored at MaizeGDB was inherited from the MaizeDB and ZmDB projects. Sequence data are from GenBank. Data are searchable by phenotype, traits, Pests, Gel Pattern, and Mutant Images. | zea mays, corn, model organism, genome, locus, metabolic pathway, genetics, genomics, sequence, gene product, function, literature reference, phenotype, trait, pest, gel pattern, mutant, blast, gene, image, corn, genotype-environment interaction, gene mapping, plant genome mapping, plant genome, gold standard, bio.tools, FASEB list |
is listed by: re3data.org is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: GenBank has parent organization: University of Maryland; Maryland; USA works with: Maize Database of Images and Genomes |
National Corn Growers Association ; NSF ; USDA/ARS ; USDA |
PMID:21624896 PMID:18769488 PMID:15888678 PMID:14681441 |
Free, Freely available, Acknowledgement requested, The community can contribute to this resource | OMICS_01655, biotools:MaizeDIG, nif-0000-03096, r3d100010795 | https://bio.tools/MaizeDIG, https://doi.org/10.17616/R3V32B | SCR_006600 | Maize Genetics and Genomics Database, MaizeGDB, MaizeGDB Locus | 2026-09-19 12:51:14 | 1047 | ||||
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Samscope Resource Report Resource Website |
Samscope (RRID:SCR_006715) | Samscope | software resource | A lightweight SAM/BAM file viewer that makes visually exploring next generation sequencing data intuitive and maybe even fun! Quickly and easily generate aggregate statistics from SAM/BAM files like coverage, polarity, and minor allele frequencies, then scroll and explore freely with a simple mouse based interface. Multiple windows can be synchronized for careful comparison across multiple experiments. | c++, visualization, opengl, next generation sequencing |
is listed by: OMICtools has parent organization: SourceForge |
GNU Affero General Public License | OMICS_00892 | SCR_006715 | samscope - A lightweight OpenGL SAM/BAM viewer | 2026-09-19 12:51:16 | 0 | |||||||
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DMEAS Resource Report Resource Website 1+ mentions |
DMEAS (RRID:SCR_006679) | DMEAS | software resource | A user-friendly DNA methylation analysis tool for DNA methylation pattern extraction, DNA methylation level estimation, DNA methylation entropy analysis and multi-sample comparison. It was developed in order to assess the DNA methylation variations for a given genomic locus or genome-wide methylation data. | c# |
is listed by: OMICtools has parent organization: SourceForge |
Creative Commons Attribution License | OMICS_00598 | SCR_006679 | DNA Methylation Entropy Analysis Software, DMEAS - DNA Methylation Entropy Analysis Software | 2026-09-19 12:51:16 | 2 | |||||||
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DeconRNASeq Resource Report Resource Website 10+ mentions |
DeconRNASeq (RRID:SCR_006713) | DeconRNASeq | software resource | An R package for deconvolution of heterogeneous tissues based on mRNA-Seq data. It modeled expression levels from heterogeneous cell populations in mRNA-Seq as the weighted average of expression from different constituting cell types and predicted cell type proportions of single expression profiles. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_01230 | SCR_006713 | 2026-09-19 12:51:16 | 44 | ||||||||||
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methVisual Resource Report Resource Website 1+ mentions |
methVisual (RRID:SCR_006705) | methVisual | software resource | Software package that allows the visualization of DNA methylation data after bisulfite sequencing. |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v2 or greater | OMICS_00604 | SCR_006705 | methVisual - Methods for visualization and statistics on DNA methylation data | 2026-09-19 12:51:16 | 1 | ||||||||
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balony Resource Report Resource Website 10+ mentions |
balony (RRID:SCR_010968) | balony | software resource | Image analysis and data inspection software for agar plates generated in high-throughput yeast genetics and genomics experiments. |
is listed by: OMICtools has parent organization: Google Code |
PMID:24305553 | OMICS_00839 | SCR_010968 | balony - Software for the analysis of high-throughput solid media-based screens | 2026-09-19 12:52:03 | 11 | ||||||||
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OligoFaktory Resource Report Resource Website 1+ mentions |
OligoFaktory (RRID:SCR_010962) | OligoFaktory | software resource | A free software for Mac OS X which designs long oligos for DNA microarrays, primers for PCR, siRNAs, and more�� | is listed by: OMICtools | Free | OMICS_00829 | SCR_010962 | 2026-09-19 12:52:03 | 1 |
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