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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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RDKit: Open-Source Cheminformatics Software Resource Report Resource Website 500+ mentions |
RDKit: Open-Source Cheminformatics Software (RRID:SCR_014274) | software resource, software toolkit | An open-source cheminformatics and machine-learning toolkit that is useable from Java or Python. It includes a collection of standard cheminformatics functionality for molecule I/O, substructure searching, chemical reactions, coordinate generation (2D or 3D), fingerprinting, etc., as well as a high-performance database cartridge for working with molecules using the PostgreSQL database. Documentation is available on the main website. | cheminformatics, machine learning, software toolkit, open source, python, c++, FASEB list |
is listed by: Debian is listed by: OMICtools |
Open source, Acknowledgement requested | OMICS_14853 | https://github.com/rdkit https://sourceforge.net/projects/rdkit/ | https://sources.debian.org/src/python3-rdkit/ | SCR_014274 | RDKit, RDKit Open-Source Cheminformatics and Machine Learning | 2026-09-19 12:58:11 | 618 | ||||||
|
imDEV Resource Report Resource Website 1+ mentions |
imDEV (RRID:SCR_014674) | software application, software resource, systems interoperability software | A software application of RExcel that integrates R into Excel as an embedded additon for omics tasks and analysis. It can be used specifically for tasks concerning multivariate data visualization, exploration, and analysis. imDev has interactive modules for dimensional reduction, prediction, feature selection, analysis of correlation, and generation of networked structures, all of which provide an integrated environment for systems level analysis of multivariate data. | statistical analysis, statistical analysis package, r, r package, excel, data visualization, feature selection, omics, systems interoperability, software, metabolomics, bio.tools |
is listed by: Metabolomics Workbench is listed by: Debian is listed by: bio.tools |
DOI:10.1093/bioinformatics/bts439 | Supports Microsoft Excel versions 2003-2010 | biotools:imdev | https://sourceforge.net/projects/imdev/, https://bio.tools/imdev | SCR_014674 | Interactive modules for Data Exploration and Visualization, Interactive modules for Data Exploration and Visualization (imDEV) | 2026-09-19 12:58:12 | 8 | ||||||
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Protein Prospector Resource Report Resource Website 500+ mentions |
Protein Prospector (RRID:SCR_014558) | software resource, software toolkit | A package of over twenty mass spectrometry-based tools primarily geared toward proteomic data analysis and database mining. It can be run from the command line, but is primarily used through a web browser, and there is a public website that allows anyone to use the software without local installation. Tandem mass spectrometry analysis tools are used for database searching and identification of peptides, including post-translationally modified peptides and cross-linked peptides. Support for isotope and label-free quantification from this type of data is provided. MS-Viewer software allows sharing and displaying of annotated spectra from many different tandem mass spectrometry data analysis packages. Other tools include software for analyzing peptide mass fingerprinting data (MS-Fit); prediction of theoretical fragmentation of peptides (MS-Product); theoretical chemical or enzymatic digestion of proteins (MS-Digest); and theoretical modeling of the isotope distribution of any chemical, including peptides (MS-Isotope). Searches using amino acid sequence can be used to identify homologous peptides in a database (MS-Pattern); the use of the combination of amino acid sequence and masses can be used for homologous peptide and protein identification using MS-Homology. Tandem mass spectrometry peak list files can be filtered for the presence of certain peaks or neutral losses using MS-Filter. Given a list of proteins, MS-Bridge can report all potential cross-linked peptide combinations of a specified mass. Given a precursor peptide mass and information about known amino acid presence, absence, or modifications, MS-Comp can report all amino acid combinations that could lead to the observed mass. | database search program, database search, database management, peptide, protein, mass spectrometry, ms, utility program, batch msms, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: University of California at San Francisco; California; USA |
Open source, Freely available to academic researchers | biotools:proteinprospector | https://bio.tools/proteinprospector | SCR_014558 | ProteinProspector | 2026-09-19 12:58:12 | 595 | |||||||
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Bionitio Resource Report Resource Website 1+ mentions |
Bionitio (RRID:SCR_017259) | software resource, software toolkit | Open source software tool to provide template for command line bioinformatics tools in various programming languages. Program reads one or more input FASTA files, computes variety of statistics on each file, and prints tabulated output. Used as basis for learning and as foundation for starting new projects. | template, command, line, bioinformatic, tool, programming, language, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: University of Melbourne; Victoria; Australia |
Free, Available for download, Freely available | biotools:bionitio | https://bio.tools/Bionitio | SCR_017259 | 2026-09-19 12:58:15 | 2 | ||||||||
|
iPiG Resource Report Resource Website |
iPiG (RRID:SCR_016164) | iPiG | software application, software resource, standalone software | Standalone software tool for the integration of peptide identifications from mass spectrometry experiments into existing genome browser visualizations. | integration, peptide, spectrum, match, genome, browser, visualization, experiment, pms, ms, bio.tools |
uses: UCSC Genome Browser is listed by: bio.tools is listed by: Debian |
Robert Koch-Institute | PMID:23226516 DOI:10.1371/journal.pone.0050246 |
Free, Available for download | biotools:ipig, OMICS_06913 | https://bio.tools/ipig, https://sources.debian.org/src/ipig/ | SCR_016164 | iPiG: Integrating Peptide Spectrum Matches Into Genome Browser Visualizations | 2026-09-19 12:58:14 | 0 | ||||
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Fastahack Resource Report Resource Website 1+ mentions |
Fastahack (RRID:SCR_016090) | software application, software resource | Software application for indexing and extracting sequences and subsequences from FASTA files. It will only generate indexes for FASTA files in which the sequences have self-consistent line lengths. | extract, quickly, subsequence, sequence, FASTA, files, generate, index |
is listed by: Debian is listed by: OMICtools |
Free, Available for download | OMICS_20516 | https://packages.debian.org/stretch/fastahack, https://sources.debian.org/src/fastahack/ | SCR_016090 | 2026-09-19 12:58:14 | 1 | ||||||||
|
Fastaq Resource Report Resource Website 10+ mentions |
Fastaq (RRID:SCR_016091) | software resource, software toolkit | Software application for diverse collection of scripts that perform useful and common FASTA/FASTQ manipulation tasks, such as filtering, merging, splitting, sorting, trimming, search/replace, etc. Input and output files can be gzipped (format is automatically detected) and individual Fastaq commands can be piped together. | diverse, script, collect, filter, merge, split, sort, trim, search, replace, file, single-letter code, nucleotide, sequence, peptide, amino acid, text-based, format |
is listed by: Debian is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Free, Available for download, Freely available | OMICS_19987 | https://sources.debian.org/src/fastaq/ | SCR_016091 | 2026-09-19 12:58:14 | 25 | ||||||||
|
Fastqtl Resource Report Resource Website 100+ mentions |
Fastqtl (RRID:SCR_016093) | Fastqtl | software resource, software toolkit | Software for mapping of molecular phenotypes that implements a new permutation scheme to accurately and rapidly correct for multiple-testing at both the genotype and phenotype levels in large-scale datasets. It is used to discover quantitative trait loci, multi-dimensional genomic datasets combining DNA-seq and ChiP-/RNA-seq. | molecular, phenotype, multiply, testing, genotype, correct, genomic dataset, trait, loci, cis, quantitative, multi dimensional |
is listed by: Debian is listed by: OMICtools has parent organization: SIB Swiss Institute of Bioinformatics |
European Commission SYSCOL FP7; European Research Council ; Helse Sør Øst ; Louis Jeantet Foundation ; NIH-NIMH (GTEx) ; Swiss National Science Foundation ; SystemsX |
PMID:26708335 | Free, Available for download | OMICS_10934 | https://sources.debian.org/src/fastqtl/ | SCR_016093 | Fastqtl: Fast quantitative trait loci | 2026-09-19 12:58:14 | 133 | ||||
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Harvest-tools Resource Report Resource Website 1+ mentions |
Harvest-tools (RRID:SCR_016132) | software resource, software toolkit | Software tools archiving and postprocessing for reference-compressed genomic multi-alignments. It is used for creating and interfacing with Gingr files, which are archives that the Harvest Suite uses to store reference-compressed multi-alignments, phylogenetic trees, filtered variants and annotations. | archiving, postprocessing, reference, compressed, genomic, multialignment, create, interface, Gingr, file, phylogentic, tree, annotation, bioinformatic, format |
is listed by: Debian is listed by: OMICtools |
Department of Homeland Security Science and Technology Directorate | PMID:25410596 | Free, Available for download, Freely available | OMICS_08468 | https://github.com/marbl/harvest-tools, https://sources.debian.org/src/harvest-tools/ | SCR_016132 | 2026-09-19 12:58:14 | 4 | ||||||
|
Alien-hunter Resource Report Resource Website 1+ mentions |
Alien-hunter (RRID:SCR_015967) | software application, software resource, standalone software | Software for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). The predictions (embl format) can be automatically loaded into Artemis genome viewer. | Horizontal Gene Transfer, Interpolated Variable Order Motifs, gene, transfer, interpolated, variable, motif, prediction, hgt, ivom |
is listed by: Debian is listed by: OMICtools works with: Artemis: Genome Browser and Annotation Tool |
Wellcome Trust | PMID:16837528 DOI:10.1093/bioinformatics/btl369 |
Free, Available for download | OMICS_08280 | https://sources.debian.org/src/alien-hunter/, https://sources.debian.org/src/alien-hunter/ | SCR_015967 | 2026-09-19 12:58:14 | 6 | ||||||
|
Bio2BEL Resource Report Resource Website 1+ mentions |
Bio2BEL (RRID:SCR_017659) | software resource, software toolkit | Software Python package enabling Biological Expression Language to act as semantic integration layer for multi modal and multi scale data sets in life sciences. Used for integrating biological databases and structured data sources in BEL. Has ability to support curation of pathway mappings, integration of pathway databases, and machine learning applications. | Biological, expression, language, integration, layer, dataset, biological, database |
uses: PyBEL is listed by: Debian is listed by: bio.tools is related to: Biological Expression Language |
DOI:10.1101/631812 | Free, Available for download, Freely available | biotools:bio2bEL, BioTools:Bio2BEL | https://github.com/bio2bel/bio2bel, https://bio.tools/Bio2BEL, https://bio.tools/Bio2BEL | SCR_017659 | 2026-09-19 12:58:16 | 7 | |||||||
|
BioBERT Resource Report Resource Website 50+ mentions |
BioBERT (RRID:SCR_017547) | software application, software resource | Pre-trained biomedical language representation model for biomedical text mining. This repository provides fine-tuning codes of BioBERT, language representation model for biomedical domain, especially designed for biomedical text mining tasks such as biomedical named entity recognition, relation extraction, question answering, etc. | Pretrained, biomedical, language, representation, model, text, mining, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: BERT |
National Research Foundation of Korea | DOI:10.1093/bioinformatics/btz682 | Free, Available for download, Freely available | biotools:biobERt | https://github.com/naver/biobert-pretrained, https://bio.tools/BioBERT | SCR_017547 | Bidirectional Encoder Representations from Transformers for Biomedical Text Mining | 2026-09-19 12:58:16 | 56 | |||||
|
MendelIHT.jl Resource Report Resource Website 1+ mentions |
MendelIHT.jl (RRID:SCR_018292) | software application, software resource | Software Julia package that implements iterative hard thresholding as multiple regression model for GWAS. Built-in support for handling PLINK and VCF files, parallel computing, fits a variety of GLM models, and handles grouping/weighting SNPs. | GWAS, iterative hard thresholding, multiple regression, GLM model, feature selection, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: PLINK |
DOI:10.1101/697755 | Free, Available for download, Freely available | biotools:mendeliht.jl | https://bio.tools/mendeliht.jl | SCR_018292 | Mendel Iterative Hard Thresholding.jl, Mendel Iterative Hard Thresholding, MendelIHT | 2026-09-19 12:58:16 | 2 | ||||||
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PhaseME Resource Report Resource Website 1+ mentions |
PhaseME (RRID:SCR_018739) | software resource, software toolkit | Software tool set to assess quality of per read phasing information and help to reduce errors during this process. | Variant Call Format Tools, quality assessment, read phasing, error, reduce error, read phasing information, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:phaseme | https://bio.tools/phaseme/ | SCR_018739 | 2026-09-19 12:58:17 | 1 | ||||||||
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BioConda Resource Report Resource Website 50+ mentions |
BioConda (RRID:SCR_018316) | software application, software resource | Software distribution management for life sciences. Channel for Conda package manager specializing in bioinformatics software. Consists of repository of recipes hosted on GitHub, build system turning these recipes into conda packages, repository of packages containing bioinformatics packages ready to use with conda install. | Software distribution management, bioinformatic software, package repository, GitHub, conda, bio.tools |
lists: CCS is listed by: bio.tools is listed by: Debian is related to: Conda is related to: RNAProt |
German Research Foundation ; Intramural Program of the National Institute of Diabetes and Digestive and Kidney Diseases ; Netherlands Organisation for Scientific Research ; NYU Abu Dhabi Research Institute |
PMID:29967506 | Free, Available for download, Freely available | biotools:bioconda | https://bio.tools/bioconda | SCR_018316 | Bioconda | 2026-09-19 12:58:16 | 73 | |||||
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CorrDrugTumorMSI Resource Report Resource Website 1+ mentions |
CorrDrugTumorMSI (RRID:SCR_018962) | software application, software resource | Software R pipeline to correlate drug distribution with tumor tissue types in mass spectrometry imaging data. | Drug, tumor heterogeneity, mass spectrometry imaging, spatial methods, drug distribution correlation, tumor tissue types, MSI, imaging data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:corrdrugtumormsi | https://bio.tools/corrdrugtumormsi | SCR_018962 | 2026-09-19 12:58:17 | 1 | ||||||||
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Chromosome Scale Assembler Resource Report Resource Website 1+ mentions |
Chromosome Scale Assembler (RRID:SCR_017960) | CSA | software application, software resource | Software pipeline for high-throughput chromosome level vertebrate genome assembly. Pipeline, which after contig assembly performs post assembly improvements by ordering assembly and closing gaps, as well as splitting of low supported regions. | Assembly, chromosome, vertebrate, genome, contig, closing, gap, splitting, low, supported, region, bio.tools |
is listed by: bio.tools is listed by: Debian |
German Research foundation | Free, Available for download, Freely available | biotools:csa2.6 | https://bio.tools/CSA2.6 | SCR_017960 | Chromosome Scale Assembler | 2026-09-19 12:58:16 | 5 | |||||
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riborex Resource Report Resource Website 1+ mentions |
riborex (RRID:SCR_019104) | software resource, software toolkit | Software R package for identification of differential translation from Ribo-seq data. Computational tool for mapping genome wide differences in translation efficiency. | Ribo-seq data, differential translation, differential translation identification, mapping genome differences, translation efficiency, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Southern California; Los Angeles; USA |
NHGRI R01 HG006015 | PMID:28158331 | Free, Available for download, Freely available | biotools:riborex | https://bio.tools/riborex | SCR_019104 | riborex v2.3.4 | 2026-09-19 12:58:18 | 7 | |||||
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Tool recommender system in Galaxy Resource Report Resource Website 1+ mentions |
Tool recommender system in Galaxy (RRID:SCR_018491) | software resource, software toolkit | Software developed by analyzing workflows composed by researchers on European Galaxy server, using deep learning approach. Used to recommend tools in Galaxy. Gated recurrent units neural network. | Recommender system, Galaxy, Workflows, Deep learning, Neural networks, Gated recurrent units, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Galaxy |
Free, Freely available | biotools:tool_recommender_system_in_galaxy | https://bio.tools/tool_recommender_system_in_galaxy | SCR_018491 | Galaxy tool recommendation, Tool recommender system in Galaxy using deep learning | 2026-09-19 12:58:17 | 2 | |||||||
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ADMIXTOOLS Resource Report Resource Website 100+ mentions |
ADMIXTOOLS (RRID:SCR_018495) | software resource, software toolkit | Software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates. | Formal test support, admixture, infer admixture proportion, infer admixture date, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Harvard University; Cambridge; United States |
NIGMS GM100233; U.S. National Science Foundation HOMINID |
PMID:22960212 | Free, Available for download, Freely available | biotools:admixtools | http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html., https://bio.tools/admixtools | SCR_018495 | 2026-09-19 12:58:17 | 222 |
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