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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Models of SHM Targeting and Substitution Resource Report Resource Website 1+ mentions |
Models of SHM Targeting and Substitution (RRID:SCR_005250) | S5F | data or information resource, data set | A targeting model that defines where mutations occur (by specifying the relative rates at which DNA motifs in the Ig sequence are mutated), and a nucleotide substitution model that defines the resulting mutation (by specifying the probability of each base mutating to each of the other three possibilities as a function of the surrounding bases). | somatic hypermutation, substitution, targeting, aid, b cell, affinity maturation, immunoglobulin, mutability, mutation, model, targeting model, nucleotide substitution model |
is listed by: OMICtools has parent organization: Yale School of Medicine; Connecticut; USA |
PMID:24298272 | Creative Commons Attribution-NonCommercial-ShareAlike License, v3 Unported | OMICS_00302 | SCR_005250 | S5F - Models of SHM Targeting and Substitution, Models of SHM Targeting and Substitution | 2026-09-19 12:58:37 | 2 | ||||||
|
SPAdes Resource Report Resource Website 100+ mentions |
SPAdes (RRID:SCR_000131) | SPAdes | software resource, software toolkit | Software package for assembling single cell genomes and mini metagenomes. Uses short read sets as input. Used for genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. Works with Illumina or IonTorrent reads and can provide hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Intended for small genomes like bacterial or fungal., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | assembler, single, cell, small, genome, short, read, data |
is used by: shovill is listed by: OMICtools is listed by: Debian is listed by: SoftCite is related to: rnaSPAdes is related to: rnaQUAST has parent organization: Saint Petersburg Academic University; Saint Petersburg; Russia works with: Illumina: iSeq 100 Sequencing System |
Government of the Russian Federation ; NCRR P41 RR024851 |
PMID:24093227 PMID:22506599 DOI:10.1089/cmb.2012.0021 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01502 | https://sources.debian.org/src/spades/ | http://bioinf.spbau.ru/spades/ | SCR_000131 | SPAdes Genome Assembler | 2026-09-19 12:55:48 | 108 | |||
|
Rosalind Resource Report Resource Website 10+ mentions |
Rosalind (RRID:SCR_006233) | Rosalind | online course, open course, training resource | A software infrastructure, course and tool set for teaching bioinformatics, and biology through the use of models. This platform for learning bioinformatics through problem solving aims to make learning bioinformatics fun and easy. Learning bioinformatics usually requires solving computational problems of varying difficulty that are extracted from real challenges of molecular biology. Rosalind offers an array of intellectually stimulating problems that grow in biological and computational complexity; each problem is checked automatically, so that the only resource required to learn bioinformatics is an internet connection. Rosalind also promises to facilitate improvements in standard bioinformatics education by providing a vital teaching aid and a central homework resource. Rosalind is inspired by Project Euler, Google Code Jam, and the ever growing movement of free online courses. The project''s name commemorates Rosalind Franklin, whose X-ray crystallography with Raymond Gosling facilitated the discovery of the DNA double helix by Watson and Crick. We hope that Rosalind will inspire a new generation of bioinformatics students by attracting biologists who want to develop vital programming skills at their own pace in a unique environment as well as programmers who have never been exposed to some of the stimulating computational problems generated by molecular biology. | bioinformatics, biology, model, programming, teaching, course, problem solving, python, algorithm, molecular biology |
is listed by: OMICtools has parent organization: University of California at San Diego; California; USA has parent organization: Saint Petersburg Academic University; Saint Petersburg; Russia |
Howard Hughes Medical Institute ; Ministry of Education and Science of the Russian Federation ; Megagrant |
nlx_151793, OMICS_01709 | SCR_006233 | 2026-09-19 12:55:48 | 39 | ||||||||
|
Koadarray Resource Report Resource Website 1+ mentions |
Koadarray (RRID:SCR_000321) | data processing software, image analysis software, software application, software resource | A fully automatic array image analysis software which can process single or multiple array images. Koadarray automatically finds the spot locations within each image and quantifies the spot intensity data. It can be used in conjunction with radioactive applications, macroarray applications, fluorescent microarray image analysis and fluorescent microplate images. | image analysis, macroarray application, fluorescent microarray, fluorescent microplate, radioactive, spot intensity data | is listed by: OMICtools | Restricted | OMICS_00842 | SCR_000321 | 2026-09-19 12:55:48 | 1 | |||||||||
|
CpGassoc Resource Report Resource Website 1+ mentions |
CpGassoc (RRID:SCR_000320) | software resource, software toolkit | Software R package to test association between methylation at CpG sites across genome and phenotype of interest, adjusting for any relevant covariates. Can perform standard analyses of large datasets without need to manually input data. Can handle mixed effects models with chip or batch entering model as random intercept. Includes tools to apply quality control filters, perform permutation tests, and create QQ plots, manhattan plots, and scatterplots for individual CpG sites. | control filters, permutation test, qq plots, manhattan plots, scatterplots, phenotype, sequence analysis software, cpg |
is listed by: OMICtools is listed by: CRAN |
PMID:22451269 | Free, Available for download, Freely available | OMICS_00793 | SCR_000320 | 2026-09-19 12:55:48 | 1 | ||||||||
|
Search Tool for Interactions of Chemicals Resource Report Resource Website 1000+ mentions |
Search Tool for Interactions of Chemicals (RRID:SCR_007947) | STITCH | data or information resource, database | Database to explore known and predicted interactions of chemicals and proteins. It integrates information about interactions from metabolic pathways, crystal structures, binding experiments and drug-target relationships. Inferred information from phenotypic effects, text mining and chemical structure similarity is used to predict relations between chemicals. STITCH further allows exploring the network of chemical relations, also in the context of associated binding proteins. Each proposed interaction can be traced back to the original data sources. The database contains interaction information for over 68,000 different chemicals, including 2200 drugs, and connects them to 1.5 million genes across 373 genomes and their interactions contained in the STRING database. | drug-target relationship, chemical, chemical-protein interaction, chemical relationship, crystal structure, metabolic pathway interaction, protein, interaction, small molecule, drug, interaction network, FASEB list |
is listed by: OMICtools is related to: Integrated Molecular Interaction Database has parent organization: European Molecular Biology Laboratory |
BMBF ; European Union FP6 EMBO ; ProBioC |
PMID:22075997 PMID:19897548 PMID:18084021 |
r3d100012165, OMICS_01589, nif-0000-03499 | https://doi.org/10.17616/R3606X, https://doi.org/10.17616/R3606X | SCR_007947 | STITCH: Chemical-Protein Interactions | 2026-09-19 12:57:13 | 1054 | |||||
|
Transterm Resource Report Resource Website 10+ mentions |
Transterm (RRID:SCR_008244) | data or information resource, database | Database that provides access to mRNA sequences and associated regulatory elements that were processed from Genbank. These mRNA sequences include complete genomes, which are divided into 5-prime UTRs, 3-prime UTRs, initiation sequences, termination regions and full CDS sequences. This data can be searched for a range of properties including specific mRNA sequences, mRNA motifs, codon usage, RSCU values, information content, etc. | element, gene, 3' utr, 5' utr, codon, genome, genomic, initiation, motif, mrna, nucleotide sequences, transcriptional regulator sites, transcription factors databases, region, regulatory, rna sequence, species, termination |
is listed by: Debian is listed by: OMICtools has parent organization: University of Otago; Dunedin; New Zealand |
DOI:10.1186/gb-2007-8-2-r22 | Public | nif-0000-21399, OMICS_06165 | https://sources.debian.org/src/transtermhp/ | http://uther.otago.ac.nz/Transterm.html | SCR_008244 | 2026-09-19 12:57:16 | 17 | ||||||
|
OMICS! OMICS! Resource Report Resource Website |
OMICS! OMICS! (RRID:SCR_008533) | OMICS! OMICS! | blog, data or information resource, narrative resource | A computational biologist''s personal views on new technologies & publications on genomics & proteomics and their impact on drug discovery. | is listed by: OMICtools | OMICS_01719 | SCR_008533 | 2026-09-19 12:57:18 | 0 | ||||||||||
|
Exon Array Analyzer Resource Report Resource Website 1+ mentions |
Exon Array Analyzer (RRID:SCR_008684) | Exon Array Analyzer | analysis service resource, data analysis service, production service resource, service resource | Service that allows you to process CEL files from Affymetrix, Inc. GeneChip Exon 1.0 ST Arrays to identify alternative splicing. | is listed by: OMICtools | OMICS_00754 | SCR_008684 | 2026-09-19 12:57:19 | 4 | ||||||||||
|
Omixon blog Resource Report Resource Website |
Omixon blog (RRID:SCR_010020) | Omixon blog | blog, data or information resource, narrative resource | We share commentaries, news and announcement that advance our goal of helping clinical labs to adopt next generation sequencing for the analysis of diagnostic gene targets. | is listed by: OMICtools | OMICS_01720 | SCR_010020 | 2026-09-19 12:57:21 | 0 | ||||||||||
|
CPSS Resource Report Resource Website 10+ mentions |
CPSS (RRID:SCR_009395) | CPSS | analysis service resource, data analysis service, production service resource, service resource | Computational Platform for analysis of Small RNA deep Sequencing data BioStaCs group., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | is listed by: OMICtools | PMID:22576177 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00355 | SCR_009395 | 2026-09-19 12:57:20 | 23 | ||||||||
|
TarBase Resource Report Resource Website 500+ mentions |
TarBase (RRID:SCR_010841) | DIANA-TarBase | data or information resource, database, service resource | Manually curated database of experimentally supported animal microRNA targets. Collection of experimentally supported miRNA gene interactions. | mirna-gene interaction |
is listed by: OMICtools is provided by: DIANA Tools |
Fondation Santé Grant ; General Secretariat of Research and Technology ; Greece Grant ; Hellenic Foundation for Research and Innovation ; IKY Foundation |
PMID:22135297 PMID:29156006 |
Restricted | OMICS_00397 | http://carolina.imis.athena-innovation.gr/diana_tools/web/index.php?r=tarbasev8%2Findex/ | SCR_010841 | DIANA-TarBase v7.0, DIANA-TarBase v.8, DIANA-TarBase v.6 | 2026-09-19 12:57:25 | 869 | ||||
|
SNPs3D Resource Report Resource Website 100+ mentions |
SNPs3D (RRID:SCR_010787) | SNPs3D | data or information resource, database | A website which assigns molecular functional effects of non-synonymous SNPs based on structure and sequence analysis. | single nucleotide polymorphism, single nucleotide variation, gene, FASEB list |
is listed by: OMICtools has parent organization: University of Maryland; Maryland; USA |
NLM | The community can contribute to this resource | OMICS_00163 | SCR_010787 | 2026-09-19 12:57:25 | 117 | |||||||
|
omiRas Resource Report Resource Website 10+ mentions |
omiRas (RRID:SCR_010833) | omiRas | analysis service resource, data analysis service, production service resource, service resource | A web server for the annotation, comparison and visualization of interaction networks of non-coding RNAs derived from small RNA-Sequencing experiments of two different conditions. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23946503 | biotools:omiras, OMICS_00383 | https://bio.tools/omiras | SCR_010833 | 2026-09-19 12:57:25 | 14 | |||||||
|
CGHweb Resource Report Resource Website 10+ mentions |
CGHweb (RRID:SCR_010923) | CGHweb | analysis service resource, data analysis service, production service resource, service resource | Data analysis service enabling users to analyse their array-CGH data with multiple algorithms simultaneously. |
is listed by: OMICtools has parent organization: Harvard Medical School; Massachusetts; USA |
OMICS_00713 | SCR_010923 | 2026-09-19 12:57:25 | 12 | ||||||||||
|
Align-GVGD Resource Report Resource Website 50+ mentions |
Align-GVGD (RRID:SCR_010772) | Align-GVGD | analysis service resource, data analysis service, production service resource, service resource | A freely available, web-based program that combines the biophysical characteristics of amino acids and protein multiple sequence alignments to predict where missense substitutions in genes of interest fall in a spectrum from enriched delterious to enriched neutral. | is listed by: OMICtools | Free | OMICS_00125 | SCR_010772 | 2026-09-19 12:57:25 | 93 | |||||||||
|
PlanTAPDB Resource Report Resource Website |
PlanTAPDB (RRID:SCR_010897) | PlanTAPDB | data or information resource, database | A phylogeny-based comprehensive database of plant transcription associated proteins. | is listed by: OMICtools | PMID:17337525 | Free | OMICS_00558 | SCR_010897 | 2026-09-19 12:57:25 | 0 | ||||||||
|
MutationTaster Resource Report Resource Website 1000+ mentions |
MutationTaster (RRID:SCR_010777) | MutationTaster | analysis service resource, data analysis service, production service resource, service resource | Evaluates disease-causing potential of sequence alterations. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
PMID:20676075 | Acknowledgement requested | biotools:mutation_taster, OMICS_00153 | https://bio.tools/mutation_taster | SCR_010777 | 2026-09-19 12:57:25 | 4781 | ||||||
|
Genomic HyperBrowser Resource Report Resource Website 10+ mentions |
Genomic HyperBrowser (RRID:SCR_010909) | Genomic HyperBrowser | analysis service resource, data analysis service, production service resource, service resource | A generic web-based system, providing statistical methodology and computing power to handle a variety of biological inquires on genomic datasets. | genomic, genomic track, gene regulation, disease association, epigenetic modification, genome |
is listed by: OMICtools has parent organization: University of Oslo; Oslo; Norway |
PMID:23632163 PMID:21182759 |
OMICS_00638 | SCR_010909 | The Genomic HyperBrowser | 2026-09-19 12:57:25 | 20 | |||||||
|
UCSC Cancer Genomics Browser Resource Report Resource Website 500+ mentions |
UCSC Cancer Genomics Browser (RRID:SCR_011796) | Cancer Genomics Browser | data or information resource, database, service resource | A suite of web-based tools to visualize, integrate and analyze cancer genomics and its associated clinical data. It is possible to display your own clinical data within one of their datasets. | genome, genomics, clinical, next-generation sequencing, chromosome, gene, FASEB list |
is listed by: OMICtools has parent organization: University of California at Santa Cruz; California; USA |
Cancer | NCI ; NHGRI ; American Association for Cancer Research ; UCSF Comprehensive Cancer Center ; California Institute for Quantitative Biosciences |
PMID:23109555 PMID:21059681 PMID:19333237 |
Acknowledgement requested | OMICS_00925 | SCR_011796 | 2026-09-19 12:57:25 | 589 |
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