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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-09-12 01:02:54 | 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 | 2026-09-12 01:02:53 | 0 | ||||
|
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 | 2026-09-12 01:02:55 | 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 | 2026-09-12 01:02:55 | 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 | 2026-09-12 01:02:55 | 2 | ||||||
|
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 | 2026-09-12 01:02:56 | 1 | ||||||||
|
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 | 2026-09-12 01:02:55 | 73 | |||||
|
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 | 2026-09-12 01:02:56 | 1 | ||||||||
|
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 | 2026-09-12 01:02:55 | 5 | |||||
|
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 | 2026-09-12 01:02:57 | 7 | |||||
|
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 | 2026-09-12 01:02:56 | 2 | |||||||
|
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 | 2026-09-12 01:02:56 | 222 | ||||||
|
CITE-seq-Count Resource Report Resource Website 50+ mentions |
CITE-seq-Count (RRID:SCR_019239) | software resource, software toolkit | Software python package that allows to count antibody TAGS from CITE-seq and/or cell hashing experiment. Software tool that allows to get UMI counts from single cell protein assay. Used to count (UMI counts) antibody-derived-tags (ADTs) or Cell Hashing tags (HTOs) in raw sequencing reads and build count matrix. | antibody TAGS count, CITE-seq, cell hashing experiment, antibody derived tags, cell hashing tags, raw sequencing reads, build count matrix, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:https:cite-seq-count | https://cite-seq.com/computational-tools/, https://bio.tools/cite-seq-count | SCR_019239 | CITE-seq-Count v1.4.0, Cellular Indexing of Transcriptomes and Epitopes by Sequencing Count | 2026-09-12 01:02:57 | 60 | |||||||
|
GeCo3 Resource Report Resource Website 1+ mentions |
GeCo3 (RRID:SCR_018877) | software application, software resource | Software tool as DNA compressor that uses neural network to do mixing of experts. | DNA compressor, neural network, expert mixing, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:geco3 | https://bio.tools/geco3 | SCR_018877 | 2026-09-12 01:02:56 | 2 | ||||||||
|
BayesEpiModels Resource Report Resource Website 1+ mentions |
BayesEpiModels (RRID:SCR_019291) | software application, software resource | Software tool for accessing performance of different epidemiological models, including both growth and compartmental models, in Bayesian framework. | Stochastic growth model, Stochastic SIR model, Bayesian inference, epidemiological models, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:bayesepimodels | https://bio.tools/bayesepimodels | SCR_019291 | 2026-09-12 01:02:57 | 1 | ||||||||
|
EpiDISH R package Resource Report Resource Website 10+ mentions |
EpiDISH R package (RRID:SCR_018004) | EpiDISH | software resource, software toolkit | Software R package provides tools to infer proportions of priori known cell-types present in sample representing mixture of such cell-types. Comparison of reference based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies. | Epigenetic, sample heterogeneity, reference, algorithm, correcting, cell type, bio.tools |
is listed by: bio.tools is listed by: Debian |
Chinese Academy of Sciences ; EU-FP7 ; Max-Planck Society ; NSFC 31571359; Royal Society Newton Advanced Fellowship ; Shanghai Institute for Biological Sciences |
PMID:28193155 | Free, Available for download, Freely available | biotools:epidish | https://github.com/sjczheng/EpiDISH, https://bio.tools/epidish | SCR_018004 | Epigenetic Dissection of Intra-Sample Heterogeneity | 2026-09-12 01:02:55 | 14 | ||||
|
SNPAAMapper Resource Report Resource Website |
SNPAAMapper (RRID:SCR_002012) | SNPAAMapper | data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. A downstream variant annotation program that can effectively classify variants by region (e.g. exon, intron, etc), predict amino acid change type (e.g. synonymous, non-synonymous mutation, etc), and prioritize mutation effects (e.g. CDS versus 5?UTR, etc). Major features: * The pipeline accepts the VCF (Variant Call Format) input file in tab-delimited format and processes the vcf input file containing all cases (G5, lowFreq, and novel) * The variant mapping step has the option of letting users select whether they want to report the bp distance between each identified intron variant and its nearby exon * The pipeline can deal with VCF files called by different SAMTools versions (0.1.18 and older ones) and also offers flexibility in dealing with vcf input files generated using SAMTools with two or three samples * The spreadsheet result file contains full protein sequences for both ref and alt alleles, which makes it easier for downstream protein structure/function analysis tools to take | single nucleotide polymorphism, amino acid, variant, annotation, exon, intron, mutation, next-generation sequencing, perl, downstream analysis, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Michigan Medical School; Michigan; USA |
PMID:24250114 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01922, biotools:snpaamapper | https://bio.tools/snpaamapper | SCR_002012 | SNPAAMapper - A SNP Amino Acid Mapping tool | 2026-09-12 01:00:53 | 0 | |||||
|
rSNP Guide Resource Report Resource Website 1+ mentions |
rSNP Guide (RRID:SCR_000087) | data or information resource, database | A system of databases which stores information on the influence of mutations in regulatory gene regions . This tool helps recognize protein binding sites that are being altered by mutation. It has four cross-linked sub databases that focus on specific aspects including: (1) the effect of single nucleotide mutations in regulatory gene regions and their interaction with nuclear proteins; (2) references to original publications on the subject; (3) the experimental details of these publications; and (4) the protocols of these experiments. This resource is aimed at providing information to further research on the influence of specific sequence alterations on disease susceptibility, drug resistance and healthcare. | database, single nucleotide mutations, RNA, DNA, nuclear proteins, protein binding sites, drug resistance, disease susceptibility, health care, regulatory gene regions, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Siberian Branch of the Russian Academy of Sciences; Novosibirsk; Russia |
Open Source | nif-0000-03428, biotools:rsnp_guide | https://bio.tools/rsnp_guide | SCR_000087 | rSNP Guide | 2026-09-12 01:01:18 | 1 | |||||||
|
Interolog/Regulog Database Resource Report Resource Website 1+ mentions |
Interolog/Regulog Database (RRID:SCR_000755) | data or information resource, database | Interolog/Regulog quantitatively assess the degree to which interologs can be reliably transferred between species as a function of the sequence similarity of the corresponding interacting proteins. | interacting, interolog, protein, regulog, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Yale University; Connecticut; USA |
PMID:15173116 | nif-0000-20863, biotools:interolog | https://bio.tools/interolog | SCR_000755 | Interolog | 2026-09-12 01:01:20 | 2 | |||||||
|
ProGlycProt Resource Report Resource Website 1+ mentions |
ProGlycProt (RRID:SCR_000622) | ProGlycProt | data or information resource, database | Manually curated, comprehensive repository of experimentally characterized bacterial glycoproteins and archaeal glycoproteins, generated from an exhaustive literature search. This is the focused effort to provide concise relevant information derived from rapidly expanding literature on prokaryotic glycoproteins, their glycosylating enzyme(s), glycosylation linked genes, and genomic context thereof, in a cross-referenced manner. The database is arranged into two sections namely, ProCGP and ProUGP. ProCGP is the main section containing characterized prokaryotic glycoproteins, defined as entries with at least one experimentally known glycosylated residue (glycosite). Whereas, ProUGP is the supplementary section, presenting uncharacterized prokaryotic glycoproteins, defined as entries with experimentally identified glycosylation but unidentified glycosites. The ProGlycProt has been developed with to aid and advance the emerging scientific interests in understanding the mechanisms, implications, and novelties of protein glycosylation in prokaryotes that include many pathogenic as well as economically important bacterial species. The website supports a dedicated structure gallery of homology models and crystal structures of characterized glycoproteins in addition to two new tools developed in view of emerging information about prokaryotic sequons (conserved sequences of amino acids around glycosites) that are never or rarely seen in eukaryotic glycoproteins. ProGlycProt provides an extensive compilation of experimentally identified glycosites (334) and glycoproteins (340) of prokaryotes that could serve as an information resource for research and technology applications in glycobiology. A general data update policy is once in three months. Existing entries are updated in real-time. | glycoprotein, glycosite, glycosylation, coding gene, protein, glycosylation type, attached glycan, oligosaccharyl transferase, glycosyl transferase, glycobiology, glycosylating enzyme, glycosylation linked gene, crystal structure, homology, homology model, blast, predict, bacteria, archaea, image collection, structure, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Institute of Microbial Technology; Chandigarh; India |
Institute of Microbial Technology; Chandigarh; India OLP0063; Council of Scientific and Industrial Research; New Delhi; India SIP10AA |
PMID:22039152 | nlx_151583, biotools:proglycprot | https://bio.tools/proglycprot | SCR_000622 | Prokaryotic Glycoproteins, ProGlycProt - A Repository of Experimentally Characterized GlycoProteins of Prokaryotes | 2026-09-12 01:01:20 | 1 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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