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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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APPRIS Resource Report Resource Website 50+ mentions |
APPRIS (RRID:SCR_012019) | APPRIS | data or information resource, database | A database that houses annotations of human splice isoforms. It adds reliable protein structural and functional data and information from cross-species conservation. A visual representation of the annotations for each gene allows users to easily identify functional changes brought about by splicing events. In addition to collecting, integrating and analyzing reliable predictions of the effect of splicing events, it also selects a single reference sequence for each gene, termed the principal isoform, based on the annotations of structure, function and conservation for each transcript. | isoform, function, annotation, splice, reference sequence, structure, conservation, transcript, FASEB list |
is listed by: OMICtools has parent organization: Spanish National Cancer Research Center |
PMID:23161672 | Free | OMICS_01881 | SCR_012019 | APPRIS - A system for annotating alternative splice isoforms | 2026-09-19 12:57:26 | 97 | ||||||
|
ENA Sequence Search Resource Report Resource Website 1+ mentions |
ENA Sequence Search (RRID:SCR_013170) | ENA Sequence Search | analysis service resource, data analysis service, production service resource, service resource | A nucleotide sequence similiary search tool which is far faster than BLAST for large datasets, with only a marginal loss in search sensitivity. | nucleotide sequencing |
is listed by: OMICtools has parent organization: European Nucleotide Archive (ENA) |
OMICS_00993 | SCR_013170 | 2026-09-19 12:57:28 | 7 | |||||||||
|
Human Transcriptome Database for Alternative Splicing Resource Report Resource Website |
Human Transcriptome Database for Alternative Splicing (RRID:SCR_013305) | H-DBAS | data or information resource, database | A specialized database for human alternative splicing (AS) based on H-Invitational full-length cDNAs. H-DBAS offers unique data and viewer for human Alternative Splicing (AS) analysis. It contains: * Genome-wide representative alternative splicing variants (RASVs) identified from following datasets * H-Inv full-length cDNAs (resource summary): H-Invitational cDNA dataset * H-Inv all transcripts (resource summary): Published human mRNA dataset * Mouse full-length cDNAs (resource summary): Mouse cDNA dataset * RASVs affecting protein functions such as protein motif, GO, subcellular localization signal and transmembrane domain * Conserved RASVs compared with mouse genome and the full-length cDNAs (H-Inv full-length cDNAs only) | alternative splicing, alternative splicing variant, cdna, transcriptome, h-invitational, rna-seq, rna, comparative genomics |
is listed by: OMICtools has parent organization: National Institute of Advanced Industrial Science and Technology |
PMID:19969536 PMID:17130147 |
nif-0000-02935, OMICS_01887 | SCR_013305 | H-DBAS - Human-transcriptome DataBase for Alternative Splicing | 2026-09-19 12:57:29 | 0 | |||||||
|
NGS Expert Blog Resource Report Resource Website |
NGS Expert Blog (RRID:SCR_013218) | NGS Expert Blog | blog, data or information resource, narrative resource | Blog including established profound know-how and proprietary protocols to cover a broad range of applications. | next generation sequencing | is listed by: OMICtools | OMICS_01718 | SCR_013218 | 2026-09-19 12:57:29 | 0 | |||||||||
|
PLAN2L Resource Report Resource Website |
PLAN2L (RRID:SCR_013346) | PLAN2L | data or information resource, database, service resource | A web-based online search system that integrates text mining and information extraction techniques to access systematically information useful for analyzing genetic, cellular and molecular aspects of the plant model organism Arabidopsis thaliana. The system facilitates a more efficient retrieval of information relevant to heterogeneous biological topics, from implications in biological relationships at the level of protein interactions and gene regulation, to sub-cellular locations of gene products and associations to cellular and developmental processes, i.e. cell cycle, flowering, root, leaf and seed development. Beyond single entities, also predefined pairs of entities can be provided as queries for which literature-derived relations together with textual evidences are returned. | text mining, bio-entity relation extraction, literature, information extraction, cell cycle, regulation, protein interaction, cellular location, flowering, leave, root, seed, gene, normalization, interaction, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Spanish National Cancer Research Center |
PMID:19520768 | OMICS_01192, biotools:plan2l | https://bio.tools/plan2l | SCR_013346 | PLAN2L: Plant Annotation to Literature, Plant annotation to literature | 2026-09-19 12:57:29 | 0 | ||||||
|
Monoclonal Antibody Index Resource Report Resource Website |
Monoclonal Antibody Index (RRID:SCR_013227) | MAI | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented September 13, 2016. A searchable biotechnology database e-books with information on more than 9000 monoclonal antibodies. This database has antibodies produced for the diagnosis and therapy of human cancer, Alzheimer's disease, AIDS, and other diseases as well as for biomarker and proteomics research. Information such as antibody name, species, type, characteristics, antigen characteristics, and developer or distributor of antibody as well as mentions in journals, patents, abstracts and reports up until 2012 are included. | antibody, monoclonal antibody, cancer, aids, sars, heart disease, vascular disease, coagulation disease, transplantation, inflammation, alzheimer's disease, autoimmunity, biomarker, proteomics, resource, research, database | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01773 | SCR_013227 | 2026-09-19 12:57:29 | 0 | ||||||||
|
DSAP Resource Report Resource Website 1+ mentions |
DSAP (RRID:SCR_013352) | DSAP | analysis service resource, data analysis service, production service resource, service resource | A web server designed to provide a total solution to analyze small RNAs sequencing data generated by SOLEXA., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20478825 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:dsap, OMICS_00357 | https://bio.tools/dsap | SCR_013352 | 2026-09-19 12:57:30 | 8 | ||||||
|
Array Designer Resource Report Resource Website 1+ mentions |
Array Designer (RRID:SCR_010960) | Array Designer | commercial organization, software resource | Oligo and cDNA Microarray Design Software that designs thousands of primers and probes for oligo and cDNA microarrays in seconds. | is listed by: OMICtools | OMICS_00825 | SCR_010960 | 2026-09-19 12:58:56 | 2 | ||||||||||
|
GeneSpring GX Resource Report Resource Website 1000+ mentions |
GeneSpring GX (RRID:SCR_010972) | GeneSpring GX | commercial organization, software resource | Powerful, accessible statistical tools for fast visualization and analysis of microarrays - expression arrays, miRNA, exon arrays and genomics copy number data. |
is listed by: OMICtools is listed by: SoftCite |
Commercial license | OMICS_00853 | SCR_010972 | 2026-09-19 12:58:56 | 1817 | |||||||||
|
miRCURY LNA microRNA Array Analysis Software Resource Report Resource Website |
miRCURY LNA microRNA Array Analysis Software (RRID:SCR_010952) | miRCURY LNA microRNA Array Analysis Software | commercial organization, software resource | Software for fast and accurate analysis of miRCURY LNA microRNA Array data. | is listed by: OMICtools | Commercial license | OMICS_00786 | SCR_010952 | 2026-09-19 12:58:56 | 0 | |||||||||
|
RTG Variant Resource Report Resource Website |
RTG Variant (RRID:SCR_010805) | rtgVariant | commercial organization, software resource | The product line encompasses distinct products for the specific needs of clinical research, saving time and money while allowing customers to focus on the answers they need most. | is listed by: OMICtools | Commercial license | OMICS_00292 | SCR_010805 | Real Time Genomics (RTG Variant) | 2026-09-19 12:58:56 | 0 | ||||||||
|
RTG Metagenomics Resource Report Resource Website |
RTG Metagenomics (RRID:SCR_011949) | rtgMetagenomics | commercial organization, software resource | Delivers comprehensive shotgun metagenomics sequence analysis for accurate species frequency composition and protein searching. | is listed by: OMICtools | Commercial license | OMICS_01522 | SCR_011949 | Real Time Genomics (RTG Metagenomics) | 2026-09-19 12:59:03 | 0 | ||||||||
|
Genomatix Solutions Resource Report Resource Website |
Genomatix Solutions (RRID:SCR_011855) | Genomatix Solutions | commercial organization, software resource | With their unique combination of proprietary algorithms and comprehensive data background, all our solutions do more than enable you to efficiently and effectively analyze and interpret biological data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools is parent organization of: Genomatix Software: Understanding Gene Regulation is parent organization of: LitInspector |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01126 | SCR_011855 | 2026-09-19 12:59:03 | 0 | |||||||||
|
Potassium Channel Database Resource Report Resource Website 1+ mentions |
Potassium Channel Database (RRID:SCR_011960) | KDB | data or information resource, data set | A Database of Potassium Ion Channel Homology Models & Molecular Dynamics Simulations. | potassium ion channel, homology model, crystal structure, molecular dynamics, simulation, structure, image |
is listed by: OMICtools has parent organization: University of Oxford; Oxford; United Kingdom |
BBSRC ; Wellcome Trust |
OMICS_01609 | SCR_011960 | Potassium Channel Database - Structures and Simulations | 2026-09-19 12:59:03 | 2 | |||||||
|
PhyloTree.org Resource Report Resource Website 100+ mentions |
PhyloTree.org (RRID:SCR_012948) | PhyloTree.org | data or information resource, data set | A phylogenetic tree of global human mitochondrial DNA variation, based on both coding- and control-region mutations, and including haplogroup nomenclature. | is listed by: OMICtools | PMID:18853457 | Free, Acknowledgement requested | OMICS_01643 | SCR_012948 | PhyloTree | 2026-09-19 12:59:14 | 370 | |||||||
|
CMA Resource Report Resource Website 10+ mentions |
CMA (RRID:SCR_012779) | CMA | commercial organization, software resource | A software package to do meta-analysis which works in a spreadsheet interface and also provides forest plots, which are useful for visualizing between-study heterogeneity. | is listed by: OMICtools | Commercial license | OMICS_00233 | SCR_012779 | Comprehensive Meta-analysis | 2026-09-19 12:59:13 | 23 | ||||||||
|
FastTree Resource Report Resource Website 5000+ mentions |
FastTree (RRID:SCR_015501) | software resource, source code | Source code that infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. It uses the Jukes-Cantor or generalized time-reversible (GTR) models of nucleotide evolution and the JTT, WAG, or LG models of amino acid evolution. | phylogenetic tree, phylogenetic tree creation, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools is related to: VeryFastTree |
PMID:19377059 DOI:10.1371/journal.pone.0009490 |
biotools:fasttree, OMICS_14703 | https://bio.tools/fasttree, https://sources.debian.org/src/fasttree/ | SCR_015501 | 2026-09-19 12:59:25 | 6279 | ||||||||
|
phytools Resource Report Resource Website 500+ mentions |
phytools (RRID:SCR_015502) | software resource, source code | Software R package for phylogenetic comparative biology. The package contains various functions for phylogenetic analysis of comparative data from species. | r package, phylogenetic comparison, phylogenetic analysis |
is listed by: Debian is listed by: OMICtools is hosted by: GitHub |
DOI:10.1111/j.2041-210X.2011.00169.x | Available for download, Acknowledgement requested | OMICS_12499 | https://github.com/liamrevell/phytools, https://sources.debian.org/src/r-cran-phytools/ | SCR_015502 | 2026-09-19 12:59:25 | 718 | |||||||
|
ProLinks Database of Functional Linkages Resource Report Resource Website |
ProLinks Database of Functional Linkages (RRID:SCR_003185) | software resource, software toolkit | THIS RESOURCE IS NO LONGER IN SERVICE, documented July 7, 2017. Collection of inference methods used to predict functional linkages between proteins. These methods include the Phylogenetic Profile method which uses the presence and absence of proteins across multiple genomes to detect functional linkages; the Gene Cluster method which uses genome proximity to predict functional linkage; Rosetta Stone which uses a gene fusion event in a second organism to infer functional relatedness; and the Gene Neighbor method which uses both gene proximity and phylogenetic distribution to infer linkage. | functional linkage, protein linkage, inference method |
is listed by: OMICtools has parent organization: University of California at Los Angeles; California; USA |
PMID:15128449 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00580 | http://prl.mbi.ucla.edu/prlbeta/prolinks.jsp http://dip.mbi.ucla.edu/dipbeta/prolinks.jsp | SCR_003185 | Prolinks | 2026-09-19 12:57:46 | 0 | ||||||
|
TherMos Resource Report Resource Website 100+ mentions |
TherMos (RRID:SCR_002790) | algorithm resource, software resource | Software used for estimating protein-DNA binding energies from in vivo binding profiles. It is a de novo motif discovery algorithm that exploits the information in transcription factor ChIP-seq or ChIP-exo datasets based on a more natural thermodynamic formalism., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | protein dna binding energy, in vivo binding profiles, motif discovery |
uses: MATLAB is listed by: OMICtools |
PMID:23595148 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00498 | SCR_002790 | 2026-09-19 12:57:46 | 208 |
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