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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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KisSplice Resource Report Resource Website 10+ mentions |
KisSplice (RRID:SCR_011893) | KisSplice | software resource, data processing software, software application, data analysis software | Software tool that enables analysis of RNA-seq data with or without reference genome. Local transcriptome assembler for SNPs, indels and AS events. | RNA-seq data analysis, with reference genome, without reference genome, local transcriptome assembler, SNPs, indels, AS events., bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1186/1471-2105-13-S6-S5 | Free, Available for download, Freely available | biotools:KisSplice, OMICS_01321 | https://bio.tools/KisSplice, https://sources.debian.org/src/kissplice/ | SCR_011893 | 2026-08-05 10:45:37 | 20 | ||||||
|
ECHO Resource Report Resource Website 100+ mentions |
ECHO (RRID:SCR_011851) | ECHO | data processing software, algorithm resource, software application, data analysis software, sequence analysis software, software resource | Error correction algorithm designed for short-reads from next-generation sequencing platforms such as Illumina''s Genome Analyzer II. | error correction, rnaseq, rna sequence, short-read, next-generation sequencing, ngs, illumina, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21482625 DOI:10.1101/gr.111351.110 |
Free, Available for download | biotools:echo, OMICS_01102 | https://bio.tools/echo, https://sources.debian.org/src/uc-echo/ | SCR_011851 | ECHO: A reference-free short-read error correction algorithm | 2026-08-05 10:45:37 | 310 | |||||
|
CANGS Resource Report Resource Website 1+ mentions |
CANGS (RRID:SCR_011837) | CANGS | software resource, data processing software, software application, data analysis software | A user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies. | windows, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
PMID:20180949 | biotools:cangs, OMICS_01084 | https://bio.tools/cangs | SCR_011837 | 2026-08-05 10:45:37 | 1 | |||||||
|
JiffyNet Resource Report Resource Website 1+ mentions |
JiffyNet (RRID:SCR_011954) | software application, simulation software, software resource, data analysis service, production service resource, service resource, analysis service resource | Web based instant protein network modeler for newly sequenced species. Web server designed to instantly construct genome scale protein networks using protein sequence data. Provides network visualization, analysis pages and solution for instant network modeling of newly sequenced species. | protein network, protein, network, genome, sequence, pathway annotation, network visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Yonsei University; Seoul; South Korea |
National Research Foundation of Korea ; Next-Generation BioGreen 21 Program |
PMID:23685435 | Free, Freely available | OMICS_01548, biotools:jiffynet | https://bio.tools/jiffynet | SCR_011954 | 2026-08-05 10:45:38 | 1 | ||||||
|
sabre Resource Report Resource Website 100+ mentions |
sabre (RRID:SCR_011843) | sabre | software resource, data processing software, software application, data analysis software | Software tool to demultiplex barcoded reads into separate files. Works on both single-end and paired-end data in fastq format. Used in next generation sequencing to analyze a broad range of data. | demultiplex, bardcode, separate, fastq, format, data, next, generation, sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:sabre, OMICS_01090 | https://bio.tools/sabre | SCR_011843 | Systems Approach to Biomarker Research | 2026-08-05 10:45:37 | 199 | ||||||
|
NGSmethDB Resource Report Resource Website 1+ mentions |
NGSmethDB (RRID:SCR_012847) | NGSmethDB | data or information resource, data repository, database, storage service resource, service resource | A dedicated database for the storage, browsing and data mining of whole-genome, single-base-pair resolution methylomes. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20965971 | OMICS_01844, biotools:ngsmethdb | https://bio.tools/ngsmethdb | SCR_012847 | NGSmethDB - A database for NGS single-cytosine-resolution DNA methylation data | 2026-08-05 10:45:53 | 9 | ||||||
|
TopHat Resource Report Resource Website 5000+ mentions Rating or validation data |
TopHat (RRID:SCR_013035) | data processing software, software application, image analysis software, alignment software, data analysis software, sequence analysis software, software resource | Software tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions. | align, RNA-Seq, read, cDNA, sequencing, transcriptomics, fast, splice, junction, mapper, exon, analysis, bio.tools |
uses: Bowtie is used by: CIRCexplorer is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: HISAT2 has parent organization: University of Maryland; Maryland; USA has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: Johns Hopkins University; Maryland; USA has parent organization: University of Washington; Seattle; USA works with: GeneScissors |
NHGRI R01 HG006102; NHGRI R01 HG006677 |
PMID:23618408 PMID:19289445 DOI:10.1093/bioinformatics/btp120 |
Free, Available for download, Freely available | biotools:tophat, OMICS_01257 | https://github.com/infphilo/tophat, https://bio.tools/tophat, https://sources.debian.org/src/tophat/ | http://tophat.cbcb.umd.edu/ | SCR_013035 | tophat, TopHat1, Tophat2 | 2026-08-05 10:45:55 | 9575 | ||||
|
MitoBreak Resource Report Resource Website 10+ mentions |
MitoBreak (RRID:SCR_012949) | MitoBreak | data or information resource, data repository, database, storage service resource, service resource | Database with curated datasets of mitochondrial DNA (mtDNA) rearrangements. Users may submit new mtDNA rearrangements. | mitochondrial dna rearrangement, mitochondrial dna, deletion, duplication, linear, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24170808 | Free, The community can contribute to this resource | biotools:mitobreak, OMICS_01640 | https://bio.tools/mitobreak | SCR_012949 | 2026-08-05 10:45:54 | 10 | ||||||
|
minfi Resource Report Resource Website 100+ mentions |
minfi (RRID:SCR_012830) | minfi | data processing software, software application, data visualization software, data analysis software, software resource | Software tools for analyzing and visualizing Illumina''s 450k array data. | Illumina, array data, Analyze Illumina Infinium DNA methylation arrays, DNA methylation array, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: SWAN has parent organization: Bioconductor |
PMID:28035024 | Free, Available for download, Freely available | biotools:minfi, OMICS_00799, BioTools:minfi | https://bio.tools/minfi, https://bio.tools/minfi, https://bio.tools/minfi | SCR_012830 | 2026-08-05 10:45:53 | 390 | ||||||
|
affy Resource Report Resource Website 1000+ mentions |
affy (RRID:SCR_012835) | Affy | software resource, data processing software, software application, data analysis software | Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis. | analysis, oligonucleotide, array, Affymetrix, process, probe, data, function, bio.tools |
is listed by: OMICtools is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: affydata is related to: R Project for Statistical Computing is related to: OMICtools |
Danish Biotechnology Instrument Center | PMID:14960456 | Free, Available for download, Freely available | BioTools:affy, OMICS_00740, biotools:affy | https://bio.tools/affy, https://sources.debian.org/src/r-bioc-affy/ | SCR_012835 | Affymetrix, analysis of Affymetrix GeneChip data at the probe level, analysis of Affymetrix GeneChip data | 2026-08-05 10:45:53 | 2996 | ||||
|
edgeR Resource Report Resource Website 10000+ mentions |
edgeR (RRID:SCR_012802) | edgeR | software resource, data processing software, software application, data analysis software | Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication. | empirical, analysis, digital, gene, expression, data, R, RNA-seq data, bio.tools |
is used by: Glimma is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: SARTools is related to: Bioconductor works with: tximport |
NHMRC 406657; Independent Research Institutes Infrastructure Support Scheme 361646; Victorian State Government OIS grant ; Melbourne International Research Scholarship ; Harris and IBS Honours scholarships |
PMID:19910308 DOI:10.1093/bioinformatics/btp616 |
Free, Available for download, Freely available | OMICS_01308, biotools:edger | https://bio.tools/edger, https://sources.debian.org/src/r-bioc-edger/ | SCR_012802 | edgeR, empirical analysis of digital gene expression data in R, Empirical analysis of Digital Gene Expression data in R | 2026-08-05 10:45:53 | 21899 | ||||
|
IMGT - the international ImMunoGeneTics information system Resource Report Resource Website 500+ mentions |
IMGT - the international ImMunoGeneTics information system (RRID:SCR_012780) | IMGT | data or information resource, portal, topical portal, database, data analysis service, production service resource, service resource, analysis service resource | A high-quality integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrate species, and in the immunoglobulin superfamily (IgSF), MHC superfamily (MhcSF) and related proteins of the immune system (RPI) of vertebrates and invertebrates, serving as the global reference in immunogenetics and immunoinformatics. IMGT provides a common access to sequence, genome and structure Immunogenetics data, based on the concepts of IMGT-ONTOLOGY and on the IMGT Scientific chart rules. IMGT works in close collaboration with EBI (Europe), DDBJ (Japan) and NCBI (USA). IMGT consists of sequence databases, genome database, structure database, and monoclonal antibodies database, Web resources and interactive tools. | immunogenetics, immunoinformatics, immunoglobulin, antibody, t cell receptor, major histocompatibility complex, immunoglobulin superfamily, major histocompatibility complex superfamily, protein, immune system, sequence, genome, structure, monoclonal antibody, gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: IMGT Repertoire has parent organization: Montpellier 2 University; Montpellier; France is parent organization of: IMGT/LIGM-DB is parent organization of: IMGT/GENE-DB is parent organization of: IMGT-ONTOLOGY is parent organization of: IMGT/V-QUEST is parent organization of: IMGT/HLA |
CNRS ; MESR ; Reseau National des Genopoles ; Region Languedoc-Roussillon ; European Union BIOMED1 BIOCT930038; European Union Biotechnology BIOTECH2 BIO4CT960037; European Union 5th PCRDT Quality of Life and Management of Living Resources QLG2-2000-01287; Agence Nationale de la recherche ANR BIOSYS06_135457; EU ImmunoGrid IST-028069 |
PMID:18978023 | nif-0000-03011, biotools:imgt | https://bio.tools/imgt | http://imgt.cines.fr | SCR_012780 | ImMunoGeneTics Information System, IMGT/LIGM, ImMunoGeneTics | 2026-08-05 10:45:52 | 746 | ||||
|
Probalign Resource Report Resource Website 10+ mentions |
Probalign (RRID:SCR_013332) | Probalign | data processing software, image analysis software, software application, alignment software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software that uses partition function posterior probability estimates to compute maximum expected accuracy multiple sequence alignments. Computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities.Produces accurate alignments on long and heterogeneous length datasets containing protein repeats. |
is used by: eProbalign is listed by: OMICtools is listed by: Debian has parent organization: New Jersey Institute of Technology; New Jersey; USA |
PMID:16954142 DOI:10.1093/bioinformatics/btl472 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00985 | https://sources.debian.org/src/probalign/ | SCR_013332 | Probalign: multiple sequence alignment using partition function posterior probabilities | 2026-08-05 10:45:54 | 16 | ||||||
|
GeneSigDB Resource Report Resource Website 10+ mentions |
GeneSigDB (RRID:SCR_013275) | GeneSigDB | data or information resource, data repository, web service, data access protocol, storage service resource, software resource, database, data analysis service, production service resource, service resource, analysis service resource | Database of traceable, standardized, annotated gene signatures which have been manually curated from publications that are indexed in PubMed. The Advanced Gene Search will perform a One-tailed Fisher Exact Test (which is equivalent to Hypergeometric Distribution) to test if your gene list is over-represented in any gene signature in GeneSigDB. Gene expression studies typically result in a list of genes (gene signature) which reflect the many biological pathways that are concurrently active. We have created a Gene Signature Data Base (GeneSigDB) of published gene expression signatures or gene sets which we have manually extracted from published literature. GeneSigDB was creating following a thorough search of PubMed using defined set of cancer gene signature search terms. We would be delighted to accept or update your gene signature. Please fill out the form as best you can. We will contact you when we get it and will be happy to work with you to ensure we accurately report your signature. GeneSigDB is capable of providing its functionality through a Java RESTful web service. | gene, gene signature, curated gene signature, gene expression, gene expression signature, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Dana-Farber Cancer Institute has parent organization: Computational Biology and Functional Genomics Laboratory at Harvard |
Cancer | Genome Research Institute ; Dana-Farber Cancer Institute ; Women's Cancers Program ; Claudia Adams Barr Foundation ; NLM 1R01 LM010129; NCI 1U19 CA148065; NHGRI 1P50 HG004233 |
PMID:22110038 | biotools:genesigdb, nlx_149342 | https://bio.tools/genesigdb | SCR_013275 | Gene Signature Data Base, GeneSigDB - Curated Gene Signatures Database | 2026-08-05 10:45:53 | 24 | ||||
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PlantNATsDB - Plant Natural Antisense Transcripts DataBase Resource Report Resource Website 1+ mentions |
PlantNATsDB - Plant Natural Antisense Transcripts DataBase (RRID:SCR_013278) | PlantNATsDB | data or information resource, database, data analysis service, production service resource, service resource, analysis service resource | Natural Antisense Transcripts (NATs), a kind of regulatory RNAs, occur prevalently in plant genomes and play significant roles in physiological and/or pathological processes. PlantNATsDB (Plant Natural Antisense Transcripts DataBase) is a platform for annotating and discovering NATs by integrating various data sources involving approximately 2 million NAT pairs in 69 plant species. PlantNATsDB also provides an integrative, interactive and information-rich web graphical interface to display multidimensional data, and facilitate plant research community and the discovery of functional NATs. GO annotation and high-throughput small RNA sequencing data currently available were integrated to investigate the biological function of NATs. A ''''Gene Set Analysis'''' module based on GO annotation was designed to dig out the statistical significantly overrepresented GO categories from the specific NAT network. PlantNATsDB is currently the most comprehensive resource of NATs in the plant kingdom, which can serve as a reference database to investigate the regulatory function of NATs. | natural antisense transcript, annotation, high-throughput, small rna sequencing, function, regulatory function, predict, sequence, small rna, blast, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: Gene Expression Omnibus has parent organization: Zhejiang University; Zhejiang; China |
National Natural Sciences Foundation of China 30971743; National Natural Sciences Foundation of China 31050110121; National Natural Sciences Foundation of China 31071659; Ministry of Science and Technology of China 2009DFA32030; Program for New Century Excellent Talents in University of China NCET-07-0740; Huazhong Agricultural University Scientific and Technological Self-innovation Foundation 2010SC07 |
PMID:22058132 | Free | nlx_151492, biotools:plantnatsdb | https://bio.tools/plantnatsdb | SCR_013278 | Plant Natural Antisense Transcripts DataBase | 2026-08-05 10:45:58 | 9 | ||||
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Dali Server Resource Report Resource Website 500+ mentions |
Dali Server (RRID:SCR_013433) | software resource, data analysis service, production service resource, service resource, analysis service resource | Network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank (PDB). You receive an email notification when the search has finished. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences. Requests can also be submitted by e-mail to dali-server at helsinki dot fi. The body of the e-mail message must contain atomic coordinates in PDB format. If you want to know the structural neighbours of a protein already in the Protein Data Bank (PDB), you can find them in the Dali Database. If you want to superimpose two particular structures, you can do it in the pairwise DaliLite server. Academic users may download the DaliLite program for local use. | Protein structure comparison server, protein structure, comparison server, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: University of Helsinki; Helsinki; Finland |
PMID:20457744 | Free, Freely available | biotools:dali | https://bio.tools/dali | SCR_013433 | Dali | 2026-08-05 10:46:01 | 509 | ||||||
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ENIGMA Resource Report Resource Website 100+ mentions |
ENIGMA (RRID:SCR_013400) | software resource, data processing software, software application, data analysis software | A software tool to extract gene expression modules from perturbational microarray data, based on the use of combinatorial statistics and graph-based clustering. The modules are further characterized by incorporating other data types, e.g. GO annotation, protein interactions and transcription factor binding information, and by suggesting regulators that might have an effect on the expression of (some of) the genes in the module. Version : ENIGMA 1.1 used GO annotation version : Aug 29th 2007 | genome, gene, genetic software, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Ghent University; Ghent; Belgium is parent organization of: ENIGMA-DTI Pipeline |
PMID:18402676 | biotools:enigma, nlx_144365 | https://bio.tools/enigma | SCR_013400 | 2026-08-05 10:46:00 | 130 | ||||||||
|
PsyGeNET Resource Report Resource Website 10+ mentions |
PsyGeNET (RRID:SCR_014406) | data or information resource, data processing software, software application, data analysis software, software resource, database | Knowledge platform on psychiatric disorders and their genes. Resource for exploratory analysis of psychiatric diseases and their associated genes. PsyGeNET is composed of database and set of analysis tools and is the result of the integration of information from DisGeNET and data extracted from the literature by text mining, followed by curation by domain experts. | psychiatric disease, associated gene, database, analysis tool, bio.tools |
is used by: DisGeNET is listed by: Debian is listed by: bio.tools |
Psychiatric disorder | DOI:10.1093/bioinformatics/btv301 | Available for the research community | biotools:psygenet2r | https://bio.tools/psygenet2r | SCR_014406 | Psychiatric disorders Gene association NETwork, Psychiatric disorders Gene association Network | 2026-08-05 10:46:09 | 11 | |||||
|
COPASI Resource Report Resource Website 100+ mentions |
COPASI (RRID:SCR_014260) | COPASI | data processing software, software application, simulation software, data analysis software, standalone software, software resource | Software application for simulation and analysis of biochemical network models and their dynamics. COPASI supports models in the SBML standard and can simulate their behavior using ODEs or Gillespies stochastic simulation algorithm. Arbitrary discrete events can be included in such simulations. Models in COPASI are based on reactions that convert a set of species into another set of species. Simulation can be performed either with stochastic kinetics or with differential equations. COPASI also includes various methods of analysis and data visualization. | standalone software, simulation software, data analysis, biochemical system simulator, biochemical network model, biochemical network dynamics, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1093/bioinformatics/btl485 | Free, Available for download, Acknowledgement requested | biotools:copasi | https://bio.tools/copasi | SCR_014260 | COPASI: Biochemical System Simulator | 2026-08-05 10:46:04 | 435 | |||||
|
CYANA Resource Report Resource Website 100+ mentions |
CYANA (RRID:SCR_014229) | software resource, data processing software, software application, data analysis software | Software for automated structure calculation of biological macromolecules on basis of conformational constraints from nuclear magnetic resonance. Program for automated NMR protein structure calculation. CYANA requires a sufficient list of assigned chemical shifts and lists of cross-peak positions and columns from 2D, 3D, or4D NOESY spectra in order to calculate the assignment of the NOESY cross-peaks and the 3D structure of the protein in solution. | protein structure, nmr, noesy, 3d structure, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Goethe University Frankfurt am Main; Hessen; Germany has parent organization: RIKEN |
PMID:15318003 PMID:25801209 |
Available to the academic community, Available to commercial user, Pay for license | SCR_021949, biotools:cyana | http://www.las.jp/english/products/cyana.html, https://bio.tools/cyana, https://dbpedia.org/page/CYANA_(software) | SCR_014229 | 2026-08-05 10:46:08 | 425 |
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