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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
METAREP Resource Report Resource Website 1+ mentions |
METAREP (RRID:SCR_011926) | METAREP | data analysis software, data processing software, software application, software resource | A tool for high-performance comparative metagenomics that allows users to view, query, browse, and compare metagenomics annotation profiles from short reads or assemblies. Users can use statistical tests, hierarchical clustering, multidimensional scaling, and heat maps to compare multiple datasets at various functional and taxonomic levels. | microbiome, comparison, comparative metagenomics, annotation, short read, short assembly, bio.tools |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian is listed by: bio.tools has parent organization: J. Craig Venter Institute |
DOI:10.1093/bioinformatics/btq455 | Open source | biotools:metarep, OMICS_01480 | https://bio.tools/metarep | SCR_011926 | 2026-09-19 12:52:21 | 8 | ||||||
|
naiveBayesCall Resource Report Resource Website |
naiveBayesCall (RRID:SCR_011866) | naiveBayesCall | software resource | An efficient model-based base-calling algorithm for high-throughput sequencing. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
OMICS_01152, biotools:bayescall | https://bio.tools/bayescall | SCR_011866 | 2026-09-19 12:52:19 | 0 | ||||||||
|
ABNER Resource Report Resource Website 10+ mentions |
ABNER (RRID:SCR_011868) | ABNER | software resource | A software tool for molecular biology text analysis. At ABNER''s core is a statistical machine learning system using linear-chain conditional random fields (CRFs) with a variety of orthographic and contextual features. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
biotools:abner, OMICS_01168 | https://bio.tools/abner | SCR_011868 | 2026-09-19 12:52:20 | 27 | ||||||||
|
Eoulsan Resource Report Resource Website 10+ mentions |
Eoulsan (RRID:SCR_011901) | Eoulsan | software resource | A versatile framework based on the Hadoop implementation of the MapReduce algorithm, dedicated to high throughput sequencing data analysis on distributed computers. | matlab, unix/linux, mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:22492314 | OMICS_01402, biotools:Eoulsan | https://www.outils.genomique.biologie.ens.fr/eoulsan/, https://bio.tools/Eoulsan | SCR_011901 | 2026-09-19 12:52:20 | 22 | |||||||
|
LitInspector Resource Report Resource Website 1+ mentions |
LitInspector (RRID:SCR_011870) | LitInspector | software resource | A literature search tool providing gene and signal transduction pathway mining within NCBI''''s PubMed database. Its sophisticated gene recognition and intuitive color coding increase the readability of abstracts and lets you analyze signal transduction pathways, diseases and tissue associations in a snap. Note: LitInspector has become part of the Literature & Pathways module of the Genomatix Software Suite. | gene, signal transduction, pathway, text-mining, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: PubMed has parent organization: Genomatix Solutions |
PMID:19417065 | OMICS_01187, biotools:litinspector | https://bio.tools/litinspector | SCR_011870 | 2026-09-19 12:52:20 | 4 | |||||||
|
AutoDock Vina Resource Report Resource Website 1000+ mentions |
AutoDock Vina (RRID:SCR_011958) | AutoDock Vina | software resource | An open-source program for doing molecular docking. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Scripps Research Institute |
PMID:34278794 PMID:19499576 DOI:10.1002/jcc.21334 |
Open unspecified license | biotools:autodock_vina, OMICS_01595, OMICS_03790 | https://bio.tools/autodock_vina, https://sources.debian.org/src/avogadro/ | SCR_011958 | 2026-09-19 12:52:21 | 2447 | ||||||
|
Orientations of Proteins in Membranes database Resource Report Resource Website 100+ mentions |
Orientations of Proteins in Membranes database (RRID:SCR_011961) | OPM | data or information resource, database, image collection | Database that provides a collection of transmembrane, monotopic and peripheral proteins from the Protein Data Bank whose spatial arrangements in the lipid bilayer have been calculated theoretically and compared with experimental data. The database allows analysis, sorting and searching of membrane proteins based on their structural classification, species, destination membrane, numbers of transmembrane segments and subunits, numbers of secondary structures and the calculated hydrophobic thickness or tilt angle with respect to the bilayer normal. | protein, membrane, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Michigan; Ann Arbor; USA |
NSF | PMID:16397007 | Acknowledgement requested | OMICS_01612, biotools:opm | https://bio.tools/opm | SCR_011961 | Orientations of Proteins in Membranes (OPM) database, OPM Database | 2026-09-19 12:52:22 | 135 | ||||
|
Scalpel Resource Report Resource Website 50+ mentions |
Scalpel (RRID:SCR_012107) | software resource | A software package for detecting INDELs (INsertions and DELetions) mutations in a reference genome which has been sequenced with next-generation sequencing technology (e.g., Illumina). | software package, c++, perl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25128977 | biotools:scalpel, OMICS_05395 | https://bio.tools/scalpel | SCR_012107 | 2026-09-19 12:52:25 | 62 | ||||||||
|
MToolBox Resource Report Resource Website 50+ mentions |
MToolBox (RRID:SCR_012112) | software resource | Software for a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25028726 | GNU General Public License | OMICS_05466, biotools:mtoolbox | https://bio.tools/mtoolbox | SCR_012112 | 2026-09-19 12:52:25 | 57 | |||||||
|
Allim Resource Report Resource Website 1+ mentions |
Allim (RRID:SCR_012114) | software resource | A user-friendly software tool to estimate allele-specific gene expression. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:23615333 | biotools:allim, OMICS_05504 | https://bio.tools/allim | SCR_012114 | 2026-09-19 12:52:25 | 2 | ||||||||
|
SNP ratio test Resource Report Resource Website 1+ mentions |
SNP ratio test (RRID:SCR_012070) | software resource | Software to calculate the number of significant SNPs in pathway divided by the number of SNPs in pathway. | standalone software, perl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:19620097 | GNU General Public License | biotools:snp_ratio_test, OMICS_04390 | https://bio.tools/snp_ratio_test | SCR_012070 | 2026-09-19 12:52:24 | 2 | |||||||
|
compomics-utilities Resource Report Resource Website 1+ mentions |
compomics-utilities (RRID:SCR_012073) | software resource | A software library containing code shared by many research projects, amongst others containing panels for visualizing spectra and chromatograms and objects for representing peptides and proteins etc. This library can be of use to other research groups doing computational proteomics. | standalone software, java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:21385435 | Apache License, v2 | OMICS_04545, biotools:compomics-utilities | https://bio.tools/compomics-utilities | SCR_012073 | 2026-09-19 12:52:24 | 5 | |||||||
|
PRIDE Converter 2 Resource Report Resource Website 1+ mentions |
PRIDE Converter 2 (RRID:SCR_012051) | software resource | Suite of software tools that allows users to convert search result files into PRIDE XML, generate mzTab skeleton files that can be used as a basis to submit quantitative and gel-based MS data, and post-process PRIDE XML files by filtering out contaminants and empty spectra. | standalone software, mac os x, unix/linux, windows, java, xml, mass spectrometry, pride, ols, proteomics, psi, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: ISA Infrastructure for Managing Experimental Metadata has parent organization: Google Code |
PMID:22949509 | Apache License, v2 | biotools:pride_converter, OMICS_03344 | https://bio.tools/pride_converter | SCR_012051 | PRIDE, PRoteomics IDEntification (PRIDE) Converter 2 | 2026-09-19 12:52:23 | 1 | ||||||
|
OpenMS Resource Report Resource Website 100+ mentions |
OpenMS (RRID:SCR_012042) | software resource | An algorithm to align LC-MS samples and to match corresponding ion species across samples. | standalone software, mac os x, unix/linux, windows, c++, python, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:17646306 DOI:10.1186/1471-2105-9-163 |
GNU Lesser General Public License | biotools:openms | https://bio.tools/openms, https://sources.debian.org/src/openms/ | SCR_012042 | 2026-09-19 12:52:23 | 184 | |||||||
|
OBI-Warp Resource Report Resource Website 1+ mentions |
OBI-Warp (RRID:SCR_012041) | software resource | Software that aligns matrices along a single axis using Dynamic Time Warping (DTW) and a one-to-one (bijective) interpolated warp function. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:16944896 | MIT License | OMICS_02386, biotools:obi-warp | https://bio.tools/obi-warp | SCR_012041 | Ordered Bijective Interpolated Warping | 2026-09-19 12:52:23 | 2 | ||||||
|
CPFP Resource Report Resource Website 1+ mentions |
CPFP (RRID:SCR_012043) | data analysis software, data processing software, software application, software resource | Software providing a data analysis pipeline for shotgun mass-spectrometry proteomics. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: University of Texas Southwestern Medical Center; Texas; USA has parent organization: University of Oxford; Oxford; United Kingdom |
PMID:20189941 | OMICS_02448, biotools:cpfp | https://bio.tools/cpfp | SCR_012043 | Central Proteomics Facilities Pipeline | 2026-09-19 12:52:23 | 7 | |||||||
|
ICPL ESIQuant Resource Report Resource Website |
ICPL ESIQuant (RRID:SCR_012047) | software resource | A proteomics software tool for quantitatively analyzing large mass spectrometric datasets acquired from ICPL based proteomics experiments. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:23454610 | biotools:icpl_esiquant, OMICS_02490 | https://bio.tools/icpl_esiquant | SCR_012047 | 2026-09-19 12:52:23 | 0 | ||||||||
|
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 | easyRNASeq - Count summarization and normalization for RNA-Seq data | 2026-09-19 12:52:22 | 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 | Visualisation of sRNAs | 2026-09-19 12:52:22 | 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 | Network Analysis and Inference Library | 2026-09-19 12:52:25 | 8 |
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