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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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easyRNASeq Resource Report Resource Website 10+ mentions |
easyRNASeq (RRID:SCR_012020) | easyRNASeq | software resource | Software that calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as ''RPKM'' or by the ''DESeq'' or ''edgeR'' package. | rna-seq, gene expression, genetics, preprocessing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor has parent organization: European Molecular Biology Laboratory |
PMID:22847932 | Artistic License, v2 | OMICS_01938, biotools:easyrnaseq | https://bio.tools/easyrnaseq | SCR_012020 | SciCrunch Registry | easyRNASeq - Count summarization and normalization for RNA-Seq data | 2026-10-10 12:39:02 | 30 | |||||
|
VisSR Resource Report Resource Website 1+ mentions |
VisSR (RRID:SCR_012024) | VisSR | data processing software, data visualization software, software application, software resource | Software to generate a visual representation of sRNAs and user-imported genomic features. The tool may be run on its own or from other tools, e.g. miRCat. |
is listed by: OMICtools is listed by: UEA sRNA Workbench is listed by: bio.tools is listed by: Debian has parent organization: University of East Anglia; Norwich; United Kingdom |
OMICS_02107, biotools:vissr | https://bio.tools/vissr | SCR_012024 | SciCrunch Registry | Visualisation of sRNAs | 2026-10-10 12:38:43 | 3 | ||||||||
|
NAIL Resource Report Resource Website 1+ mentions |
NAIL (RRID:SCR_012134) | software resource | A set of software tools to simplify the range of computational activities involved in regulatory network inference. It is technology-independent and includes an interface layer to allow easy integration of components into other applications. It is implemented in MATLAB and is available for all researchers to use. | standalone software, mac os x, unix/linux, windows, matlab, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25246431 | Apache License | OMICS_05868, biotools:nail | https://bio.tools/nail | SCR_012134 | SciCrunch Registry | Network Analysis and Inference Library | 2026-10-10 12:39:04 | 8 | ||||||
|
LocalAli Resource Report Resource Website 1+ mentions |
LocalAli (RRID:SCR_012147) | software resource | A fast and scalable local network alignment software tool for the identification of functionally conserved modules in multiple networks. LocalAli outperforms all existing algorithms in terms of coverage, consistency and scalability, meanwhile retains a high precision in the identification of functionally coherent subnetworks. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:25282642 | GNU General Public License | biotools:localali, OMICS_06337 | https://bio.tools/localali | SCR_012147 | SciCrunch Registry | 2026-10-10 12:39:04 | 1 | |||||||
|
IMGT-ONTOLOGY Resource Report Resource Website 1+ mentions |
IMGT-ONTOLOGY (RRID:SCR_010342) | IMGT-ONTOLOGY | controlled vocabulary, data or information resource, ontology | Ontology for immunogenetics and immunoinformatics. Provides semantic specification of terms to be used in immunogenetics and immunoinformatics and manages related knowledge, thus allowing standardization for immunogenetics data from genome, proteome, genetics, two-dimensional (2D) and three-dimensional (3D) structures. Manages the knowledge through diverse facets relying on seven axioms, IDENTIFICATION, CLASSIFICATION, DESCRIPTION, NUMEROTATION, LOCALIZATION, ORIENTATION and OBTENTION. These axioms postulate that any object, any process and any relation can be identified, classified, described, numbered, localized and orientated, and the way it is obtained can be characterized. The axioms constitute the Formal IMGT-ONTOLOGY, also designated as IMGT-Kaleidoscope. As the same axioms can be used to generate concepts for multi-scale level approaches, the Formal IMGT-ONTOLOGY represents a paradigm for system biology ontologies, which need to identify, to classify, to describe, to number, to localize and to orientate objects, processes and relations at the molecule, cell, tissue, organ, organism or population levels. IMGT, the international ImMunoGeneTics information system, has been built on IMGT-ONTOLOGY. The version 1.0.2 of IMGT-ONTOLOGY includes the concepts of IDENTIFICATION and the concepts of CLASSIFICATION. | owl, ontology, immunogenetics, immunoinformatics, terms semantic specification, bio.tools |
is listed by: BioPortal is listed by: Debian is listed by: bio.tools has parent organization: IMGT - the international ImMunoGeneTics information system |
Free, Freely available | nlx_157436, biotools:IMGt-ONtOLOGY | http://www.imgt.org/IMGTindex/ontology.php, https://bio.tools/IMGT-ONTOLOGY | SCR_010342 | SciCrunch Registry | 2026-10-10 12:38:12 | 2 | |||||||
|
SOAPsnp Resource Report Resource Website 100+ mentions |
SOAPsnp (RRID:SCR_010602) | SOAPsnp | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software providng a method based on Bayes? theorem (the reverse probability model) to call consensus genotype by carefully considering the data quality, alignment, and recurring experimental errors., 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 |
DOI:10.1101/gr.088013.108 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:soapsnp, OMICS_00078 | https://bio.tools/soapsnp, https://sources.debian.org/src/soapsnp/ | SCR_010602 | SciCrunch Registry | 2026-10-10 12:38:35 | 207 | ||||||
|
MIRA Resource Report Resource Website 1000+ mentions |
MIRA (RRID:SCR_010731) | MIRA | software resource | Sequence assembler and mapper for whole genome shotgun and EST/RNASeq sequencing data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge is required by: MITObim |
PMID:15140833 DOI:10.1101/gr.1917404 |
OMICS_00023, biotools:mira | https://bio.tools/mira | https://sources.debian.org/src/mira-assembler/ | SCR_010731 | SciCrunch Registry | Mimicking Intelligent Read Assembly | 2026-10-10 12:38:36 | 1047 | |||||
|
Crux tandem mass spectrometry analysis software Resource Report Resource Website 10+ mentions |
Crux tandem mass spectrometry analysis software (RRID:SCR_010648) | software resource | A software toolkit for tandem mass spectrometry analysis, with a focus on peptide identification. Crux analyzes shotgun proteomics tandem mass spectra, associating peptides with observed spectra. This software toolkit for tandem mass spectrometry analysis, with a focus on peptide identification is provided as a single executable. Crux is implemented in C and is distributed with source code freely to noncommercial users. Mass spectrometry, the core technology in the field of proteomics, promises to enable scientists to identify and quantify the entire complement of proteins in a complex biological sample. Currently, the primary bottleneck in this type of experiment is computational. Existing algorithms for interpreting mass spectra are slow and fail to identify a large proportion of the given spectra. We describe a database search program called Crux that reimplements and extends the widely used database search program Sequest. For speed, Crux uses a peptide indexing scheme to rapidly retrieve candidate peptides for a given spectrum. For each peptide in the target database, Crux generates shuffled decoy peptides on the fly, providing a good null model and, hence, accurate false discovery rate estimates. Crux also implements two recently described postprocessing methods: a p value calculation based upon fitting a Weibull distribution to the observed scores, and a semisupervised method that learns to discriminate between target and decoy matches. Both methods significantly improve the overall rate of peptide identification. | proteomics, software toolkit, source code, bio.tools |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools has parent organization: University of Washington; Seattle; USA |
PMID:18505281 DOI:10.1021/pr500741y |
nlx_66678, biotools:crux | https://bio.tools/crux | https://sources.debian.org/src/crux-toolkit/ | SCR_010648 | SciCrunch Registry | Crux | 2026-10-10 12:38:16 | 34 | ||||||
|
Evex Resource Report Resource Website 10+ mentions |
Evex (RRID:SCR_010509) | data or information resource, database, software application, software resource, text-mining software | EVEX is a text mining resource built on top of PubMed abstracts and PubMed Central full texts. It contains over 40 million bio-molecular events among more than 76 million automatically extracted gene/protein name mentions. The text mining data further has been enriched with gene normalization results, allowing straightforward integration with external resources. Further, gene families from Ensembl and HomoloGene provide homology-based event generalizations. EVEX presents both direct and indirect associations between genes and proteins, enabling explorative browsing of relevant literature. | gene, protein, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Ghent University; Ghent; Belgium |
biotools:evex, nlx_158731 | https://bio.tools/evex | SCR_010509 | SciCrunch Registry | 2026-10-10 12:38:15 | 19 | |||||||||
|
SNPinfo Web Server Resource Report Resource Website 100+ mentions |
SNPinfo Web Server (RRID:SCR_010589) | service resource | SNPinfo Web Server is a set of freely available web-based SNP selection tools where investigators can specify genes or linkage regions and select SNPs based on GWAS results, linkage disequilibrium (LD), and predicted functional characteristics of both coding and non-coding SNPs. The algorithm uses GWAS SNP P-value data and finds all SNPs in high LD with GWAS SNPs, so that selection is from a much larger set of SNPs than the GWAS itself. The program can also identify and choose tag SNPs for SNPs not in high LD with any GWAS SNP. We incorporate functional predictions of protein structure, gene regulation, splicing and miRNA binding, and consider whether the alternative alleles of a SNP are likely to have differential effects on function. Users can assign weights for different functional categories of SNPs to further tailor SNP selection. The program accounts for LD structure of different populations so that a GWAS study from one ethnic group can be used to choose SNPs for one or more other ethnic groups. SNP Selection and Functional Information *Candidate Gene SNP Selection (GenePipe):SNP selection for candidate genes based on Genome Wide Association Study (GWAS) results, functional SNP prediction and Linkage Disequilibrium (LD) information. *GWAS Functional SNP Selection (GenomePipe):Functional SNP selection from SNPs that are in high LD with GWAS SNPs *GWAS SNP Selection in Linkage Loci (LinkagePipe):GWAS SNP selection in candidate genomic regions (such as linkage loci) *LD TAG SNP Selection (TagSNP):LD tag SNP selection and visualization for single or multiple populations. Finalization of SNP list from various queries. *SNP Function Prediction (FuncPred): Querying SNP function predictions and ethnic-specific allele frequencies. *SNP Information in DNA Sequence (SNPseq):Visualization of SNP related information in the context of DNA sequence. Preparing DNA Sequence for PCR Primer Design considering SNP information. Detailed information of CpG region. | bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: National Institute of Environmental Health Sciences |
PMID:19417063 | nlx_46274, biotools:snpinfo | https://bio.tools/snpinfo | SCR_010589 | SciCrunch Registry | 2026-10-10 12:38:15 | 254 | ||||||||
|
EULER-SR Resource Report Resource Website 10+ mentions |
EULER-SR (RRID:SCR_010485) | EULER-SR | software resource | Assembly package that contains a suite of software programs for correcting errors in short reads and assembling them. The assembler may take as input classical Sanger reads, 454 sequences, and Illumina reads. | fragment assembly, short read, read |
is listed by: OMICtools is listed by: Debian has parent organization: University of California at San Diego; California; USA |
PMID:18083777 DOI:10.1101/gr.7088808 |
OMICS_00015 | http://ngslib.i-med.ac.at/node/64, https://sources.debian.org/src/euler-sr/ | SCR_010485 | SciCrunch Registry | EULER: short reads assembler | 2026-10-10 12:38:14 | 17 | ||||||
|
miRDB Resource Report Resource Website 1000+ mentions |
miRDB (RRID:SCR_010848) | miRDB | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | An online database for miRNA target prediction and functional annotations. | mirna, target, pathway, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:18426918 PMID:18048393 |
OMICS_00403, biotools:miRDb | https://bio.tools/miRDB | SCR_010848 | SciCrunch Registry | 2026-10-10 12:38:33 | 2027 | |||||||
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SICER Resource Report Resource Website 100+ mentions |
SICER (RRID:SCR_010843) | SICER | software resource | A clustering software package for identification of enriched domains from histone modification ChIP-Seq data. | python, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: George Washington University; Washington D.C.; USA |
PMID:19505939 | biotools:sicer, OMICS_00461 | https://bio.tools/sicer | SCR_010843 | SciCrunch Registry | SICER: A clustering approach for identification of enriched domains from histone modification ChIP-Seq data | 2026-10-10 12:38:32 | 420 | ||||||
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MapSplice Resource Report Resource Website 100+ mentions |
MapSplice (RRID:SCR_010844) | MapSplice | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. Accurate mapping of RNA-seq reads for splice junction discovery. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Kentucky; Kentucky; USA |
PMID:20802226 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mapsplice, OMICS_01243 | https://bio.tools/mapsplice | SCR_010844 | SciCrunch Registry | 2026-10-10 12:38:19 | 214 | ||||||
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QSRA Resource Report Resource Website 1+ mentions |
QSRA (RRID:SCR_010733) | QSRA | software resource | A quality-value guided de novo short read assembler. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00026, biotools:qsra | https://bio.tools/qsra | SCR_010733 | SciCrunch Registry | 2026-10-10 12:38:17 | 1 | ||||||||
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HARSH Resource Report Resource Website 10+ mentions |
HARSH (RRID:SCR_010792) | HARSH | software resource | Software that provides a method to infer the haplotype using haplotype reference panel and high throughput sequencing data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at Los Angeles; California; USA |
OMICS_00199, biotools:harsh | https://bio.tools/harsh | SCR_010792 | SciCrunch Registry | HAplotype inference using Reference and Sequencing tecHnology | 2026-10-10 12:38:18 | 15 | |||||||
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HapFABIA Resource Report Resource Website 1+ mentions |
HapFABIA (RRID:SCR_010793) | HapFABIA | software resource | Software that identifies short identity by descent (IBD) segments that are tagged by rare variants in large sequencing data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Johannes Kepler University of Linz; Linz; Austria |
PMID:24174545 | biotools:hapfabia, OMICS_00203 | https://bio.tools/hapfabia | SCR_010793 | SciCrunch Registry | HapFABIA: Identification of very short segments of identity by descent characterized by rare variants in large sequencing data | 2026-10-10 12:38:37 | 3 | ||||||
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Pedimap Resource Report Resource Website 10+ mentions |
Pedimap (RRID:SCR_010796) | Pedimap | software resource | A software tool for visualizing phenotypic and genotypic data for related individuals linked in pedigrees. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23087384 | OMICS_00214, biotools:pedimap | https://bio.tools/pedimap | SCR_010796 | SciCrunch Registry | 2026-10-10 12:38:18 | 11 | |||||||
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CEQer Resource Report Resource Website 1+ mentions |
CEQer (RRID:SCR_010813) | CEQer | software resource | A graphical, event-driven tool for CNA/AI-coupled analysis of exome sequencing reads. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24124457 | Commercial license, Free | biotools:ceqer, OMICS_00329 | https://bio.tools/ceqer | SCR_010813 | SciCrunch Registry | Comparative Exome Quantification analyzer | 2026-10-10 12:38:38 | 7 | |||||
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Oncodrive-fm Resource Report Resource Website 10+ mentions |
Oncodrive-fm (RRID:SCR_010781) | Oncodrive-fm | software resource | An approach to uncover driver genes or gene modules. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00157, biotools:oncodrivefm | https://bio.tools/oncodrivefm | SCR_010781 | SciCrunch Registry | 2026-10-10 12:38:31 | 15 |
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