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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MMSEQ Resource Report Resource Website 50+ mentions |
MMSEQ (RRID:SCR_008184) | MMSEQ | software resource | Software package that contains a collection of statistical tools for analysing RNA-seq expression data. | is listed by: OMICtools | PMID:24281695 | OMICS_01280 | SCR_008184 | 2026-08-08 11:59:13 | 66 | |||||||||
|
Seven Bridges Genomics Resource Report Resource Website 1+ mentions |
Seven Bridges Genomics (RRID:SCR_008308) | Seven Bridges | service resource | A cloud platform for next-generation sequencing analysis. | next generation sequencing, cloud computing | is listed by: OMICtools | OMICS_01222 | SCR_008308 | 2026-08-08 11:59:14 | 4 | |||||||||
|
ChroMoS Resource Report Resource Website 1+ mentions |
ChroMoS (RRID:SCR_008320) | ChroMoS | software resource | Combines genetic and epigenetic data to facilitate SNP classification, prioritization and prediction of their functional effect. | Chromatin, modified SNPs, SNPs, genetic and epigenetic data combination | is listed by: OMICtools | PMID:23782616 | Free, Freely available | OMICS_00145 | SCR_008320 | Chromatin Modified SNPs | 2026-08-08 11:59:07 | 5 | ||||||
|
VAMP Resource Report Resource Website 50+ mentions |
VAMP (RRID:SCR_008527) | VAMP | software resource | Software for visualization and Analysis of CGH arrays, transcriptome and other Molecular Profiles. |
is listed by: OMICtools has parent organization: Curie Institute; Paris; France |
PMID:16820431 | OMICS_00738 | SCR_008527 | VAMP: Visualization and Analysis of CGH arrays transcriptome and other Molecular Profiles, Visualization and Analysis of array-CGH transcriptome and other Molecular Profiles | 2026-08-08 11:59:10 | 71 | ||||||||
|
DEGseq Resource Report Resource Website 1000+ mentions |
DEGseq (RRID:SCR_008480) | DEGseq | software resource | R package to identify differentially expressed genes from RNA-Seq data. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_01305 | SCR_008480 | 2026-08-08 11:59:16 | 1729 | ||||||||||
|
EMBOSS Resource Report Resource Website 1000+ mentions |
EMBOSS (RRID:SCR_008493) | EMBOSS | sequence analysis software, software toolkit, software resource, software application, data analysis software, data processing software | Software analysis package for molecular biology community. Automatically copes with data in variety of formats and allows transparent retrieval of sequence data from web. Libraries are provided with package. Provides toolkit for creating bioinformatics applications or workflows. Provides set of sequence analysis programs. Provided programs cover areas such as sequence alignment, rapid database searching with sequence patterns, protein motif identification, nucleotide sequence pattern analysis, codon usage analysis for small genomes, rapid identification of sequence patterns in large scale sequence sets, and presentation tools for publication. | FASEB list |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite is related to: BioExtract is related to: pepwheel |
DOI:10.1016/S0168-9525(00)02024-2 | Free, Freely available | OMICS_21165, nif-0000-30488 | https://sources.debian.org/src/emboss/ | http://www.emboss.org | SCR_008493 | The European Molecular Biology Open Software Suite, European Molecular Biology Open Software Suite | 2026-08-08 11:59:03 | 4742 | ||||
|
World Health Organization Resource Report Resource Website 1000+ mentions |
World Health Organization (RRID:SCR_008505) | WHO | nonprofit organization | The directing and coordinating authority responsible for public health within the United Nations system. The WHO Regional Office for Europe (WHO/Europe) is one of the six regional offices around the world. It serves the WHO European Region, which comprises 53 countries from the Atlantic to the Pacific oceans. WHO/Europe collaborates with a range of public health stakeholders in the Region and globally, to ensure that coordinated action is taken to develop and implement efficient health policies and to strengthen health systems. WHO/Europe is made up of public health, scientific, and technical experts. |
is listed by: OMICtools is parent organization of: World Health Organization: The Global Health Library is parent organization of: WHO International Clinical Trials Registry Platform is parent organization of: International Agency for Research on Cancer is parent organization of: World Health Organization Statistical Information System is parent organization of: WHO Adverse Reaction Terminology is parent organization of: WHO World Health Mental Health Surveys |
Wikidata: Q7817, grid.3575.4, ISNI: 121633745, nif-0000-30534, Crossref funder ID: 100004423 | https://ror.org/01f80g185 | SCR_008505 | 2026-08-08 11:59:03 | 3572 | |||||||||
|
tRNAscan-SE Resource Report Resource Website 1000+ mentions |
tRNAscan-SE (RRID:SCR_008637) | web application, production service resource, software resource, data analysis service, analysis service resource, service resource | Web server to search for tRNA genes in genomic sequence. If you would like to run tRNAscan-SE locally, you can get the UNIX source code (gzip''d tar file). | bio.tools, tRNA genes, genomic sequence |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools has parent organization: University of California at Santa Cruz; California; USA |
PMID:15980563 PMID:9023104 DOI:10.1093/nar/25.5.0955 |
Free, Freely available | SCR_010835, OMICS_00385, nif-0000-32031, biotools:trnascan-se | https://bio.tools/trnascan-se, https://sources.debian.org/src/trnascan-se/ | SCR_008637 | Lowe Lab tRNAscan-SE | 2026-08-08 11:59:18 | 2855 | ||||||
|
DMI Resource Report Resource Website |
DMI (RRID:SCR_008599) | DMI | software resource | Computational tool developed to help identify cancer-associated ''driver'' mutations from ''passenger'' ones in a cancer genome. | is listed by: OMICtools | Cancer | OMICS_00148 | SCR_008599 | Driver Mutation Identification | 2026-08-08 11:59:18 | 0 | ||||||||
|
Ingenuity Pathway Analysis Resource Report Resource Website 5000+ mentions Rating or validation data |
Ingenuity Pathway Analysis (RRID:SCR_008653) | IPA | pathway analysis tool | A web-based software application that enables users to analyze, integrate, and understand data derived from gene expression, microRNA, and SNP microarrays, metabolomics, proteomics, and RNA-Seq experiments, and small-scale experiments that generate gene and chemical lists. Users can search for targeted information on genes, proteins, chemicals, and drugs, and build interactive models of experimental systems. IPA allows exploration of molecular, chemical, gene, protein and miRNA interactions, creation of custom molecular pathways, and the ability to view and modify metabolic, signaling, and toxicological canonical pathways. In addition to the networks and pathways that can be created, IPA can provide multiple layering of additional information, such as drugs, disease genes, expression data, cellular functions and processes, or a researchers own genes or chemicals of interest. | software, drug, gene, analysis, chemical, metabolic, model, pathway, protein, signal, molecular signaling, genomic, pathway analysis tool |
uses: Ingenuity Pathways Knowledge Base is listed by: Biositemaps is listed by: OMICtools is listed by: SoftCite |
Commercial license | nif-0000-33144, OMICS_00399 | http://www.ingenuity.com/products/ipa, http://www.ingenuity.com/products/ipa/microrna-research | SCR_008653 | QIAGEN Ingenuity Pathway Analysis | 2026-08-08 11:59:18 | 6828 | ||||||
|
Tute Genomics Resource Report Resource Website |
Tute Genomics (RRID:SCR_008672) | Tute Genomics | service resource | A robust, secure, medical-grade, web application that lives in the cloud and has the ability to analyze and annotate entire human genomes in a rapid and cost-effective way. | genome, cloud computing | is listed by: OMICtools | OMICS_01223 | SCR_008672 | 2026-08-08 11:59:13 | 0 | |||||||||
|
eXtasy Resource Report Resource Website 1+ mentions |
eXtasy (RRID:SCR_008671) | eXtasy | software resource | A pipeline for ranking nonsynonymous single nucleotide variants given a specific phenotype. | is listed by: OMICtools | OMICS_00150 | SCR_008671 | 2026-08-08 11:59:06 | 4 | ||||||||||
|
Condel Resource Report Resource Website 100+ mentions |
Condel (RRID:SCR_008584) | Condel | software resource | A method to assess the outcome of nonsynonymous SNVs using a consensus deleteriousness score that combines various tools (e.g. SIFT, Polyphen2, MutationAssessor). | is listed by: OMICtools | OMICS_00146 | SCR_008584 | CONsensus DELeteriousness score of missense SNVs | 2026-08-08 11:59:04 | 222 | |||||||||
|
DWD Resource Report Resource Website |
DWD (RRID:SCR_008760) | DWD | software resource | This software package provides the implementation of distance weighted discrimination (DWD) using an interior point method for the solution of second order cone programming problems. | is listed by: OMICtools | OMICS_00858 | SCR_008760 | 2026-08-08 11:59:07 | 0 | ||||||||||
|
RUM Resource Report Resource Website 1+ mentions |
RUM (RRID:SCR_008818) | RUM | software resource | An alignment, junction calling, and feature quantification pipeline specifically designed for Illumina RNA-Seq data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
OMICS_01249, biotools:rum | https://bio.tools/rum, https://github.com/itmat/rum/wiki | SCR_008818 | Rna seq Unified Mapper | 2026-08-08 11:59:16 | 7 | |||||||
|
miR-PREFeR Resource Report Resource Website 1+ mentions |
miR-PREFeR (RRID:SCR_003353) | software resource | An accurate, fast, and easy-to-use plant miRNA prediction software tool using small RNA-Seq data. It utilizes expression patterns of miRNA and follows the criteria for plant microRNA annotation to accurately predict plant miRNAs from one or more small RNA-Seq data samples of the same species. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24930140 | Free, Available for download, Freely available | biotools:mir-prefer, OMICS_04637 | https://bio.tools/mir-prefer | SCR_003353 | miRNA PREdiction From small RNA-Seq data, miR-PREFeR: microRNA PREdiction From small RNAseq data | 2026-08-08 11:58:03 | 8 | ||||||
|
PicTar Resource Report Resource Website 1000+ mentions |
PicTar (RRID:SCR_003343) | PicTar | software resource | An algorithm for the identification of microRNA targets. Details are provided (3' UTR alignments with predicted sites, links to various public databases etc) regarding: # microRNA target predictions in vertebrates (Krek et al, Nature Genetics 37:495-500 (2005)) # microRNA target predictions in seven Drosophila species (Grn et al, PLoS Comp. Biol. 1:e13 (2005)) # microRNA targets in three nematode species (Lall et al, Current Biology 16, 1-12 (2006)) # human microRNA targets that are not conserved but co-expressed (i.e. the microRNA and mRNA are expressed in the same tissue) (Chen and Rajewsky, Nat Genet 38, 1452-1456 (2006)) co-expressed targets | microrna target, microrna, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: UCSC Genome Browser has parent organization: Max Delbruck Center for Molecular Medicine; Berlin; Germany |
PMID:15806104 | Free, Available for download, Freely available | OMICS_00411, biotools:pictar, nif-0000-31983 | http://pictar.mdc-berlin.de/, https://bio.tools/pictar | SCR_003343 | 2026-08-08 11:57:58 | 1717 | ||||||
|
BlockClust Resource Report Resource Website 1+ mentions |
BlockClust (RRID:SCR_003347) | software resource | Software for efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles. | is listed by: OMICtools | PMID:24931994 | Free, Available for download, Freely available | OMICS_04641 | SCR_003347 | 2026-08-08 11:57:56 | 1 | |||||||||
|
EasyqpcR Resource Report Resource Website 1+ mentions |
EasyqpcR (RRID:SCR_003406) | EasyqpcR | software resource, software application, data analysis software, data processing software | Software package for low-throughput real-time quantitative PCR data analysis. The package allows you to import easily qPCR data files. Thereafter, you can calculate amplification efficiencies, relative quantities and their standard errors, normalization factors based on the best reference genes choosen (using the SLqPCR package), and then the normalized relative quantities, the NRQs scaled to your control and their standard errors. | qpcr, gene expression |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02313 | https://www.bioconductor.org/packages//2.13/bioc/html/EasyqpcR.html | SCR_003406 | 2026-08-08 11:57:59 | 9 | |||||||
|
PLANTTFDB Resource Report Resource Website 1000+ mentions |
PLANTTFDB (RRID:SCR_003362) | PlantTFDB | data or information resource, production service resource, data analysis service, database, analysis service resource, service resource | Comprehensive plant transcription factor database. Interface to allow users to search the database by IDs or free texts, to make sequence similarity search against TFs of all or individual species, and to download TF sequences for local analysis.PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors | transcription factor, expression, regulation, interaction, conserved element, phenotype, function, evolution, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Database of Poplar Transcription Factors is related to: Plant Ontology has parent organization: Peking University; Beijing; China |
China 863 ; China 973 ; NSFC ; China NSFC |
PMID:24174544 PMID:17933783 PMID:21097470 |
Free, Available for download, Freely available | nif-0000-03311, biotools:planttfdb_2.0, OMICS_00560, r3d100010137 | https://bio.tools/planttfdb_2.0, https://doi.org/10.17616/R3JG6V | http://planttfdb.cbi.pku.edu.cn | SCR_003362 | , PlantTFDB 2.0, Plant Transcription Factor Database | 2026-08-08 11:58:04 | 1441 |
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