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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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 | ||||||||
|
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 | |||||
|
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 | ||||||||
|
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 | |||||
|
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 | |||||
|
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 | |||||||
|
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 | ||||||
|
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 | 2026-09-19 12:58:18 | 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 | 2026-09-19 12:58:17 | 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 | 2026-09-19 12:58:18 | 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 | 2026-09-19 12:58:16 | 14 | ||||
|
TomoMiner Resource Report Resource Website 1+ mentions |
TomoMiner (RRID:SCR_015045) | software resource, source code | Software platform for large-scale cryo electron subtomogram classification, alignment, and averaging. | analysis platform, cryo electron subtomogram, subtomogram classification, subtomogram alignment, subtomogram averaging, subtomogram analysis, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Southern California; Los Angeles; USA requires: Python Programming Language requires: NumPy requires: SciPy requires: LAPACK linear algebra library requires: Cython C-Extensions for Python |
Available for download | biotools:tomominer | https://bio.tools/tomominer | SCR_015045 | 2026-09-19 12:59:16 | 3 | ||||||||
|
GO2MSIG Resource Report Resource Website 1+ mentions |
GO2MSIG (RRID:SCR_018359) | data or information resource, data set |
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 24, 2020. Software tool as automated Gene Ontology based multi species gene set generator for gene set enrichment analysis. Used to generate gene sets required for Gene Set Enrichment Analysis for almost any organism for which GO term association data exists. Gene set collections can be automatically created for wide variety of species. |
bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Broad Institute |
PMID:24884810 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:go2msig | https://bio.tools/go2msig | http://www.go2msig.org/cgi-bin/go2msig.cgi | SCR_018359 | 2026-09-19 12:59:35 | 6 | ||||||
|
FastTree Resource Report Resource Website 5000+ mentions |
FastTree (RRID:SCR_015501) | software resource, source code | Source code that infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. It uses the Jukes-Cantor or generalized time-reversible (GTR) models of nucleotide evolution and the JTT, WAG, or LG models of amino acid evolution. | phylogenetic tree, phylogenetic tree creation, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools is related to: VeryFastTree |
PMID:19377059 DOI:10.1371/journal.pone.0009490 |
biotools:fasttree, OMICS_14703 | https://bio.tools/fasttree, https://sources.debian.org/src/fasttree/ | SCR_015501 | 2026-09-19 12:59:25 | 6279 | ||||||||
|
phytools Resource Report Resource Website 500+ mentions |
phytools (RRID:SCR_015502) | software resource, source code | Software R package for phylogenetic comparative biology. The package contains various functions for phylogenetic analysis of comparative data from species. | r package, phylogenetic comparison, phylogenetic analysis |
is listed by: Debian is listed by: OMICtools is hosted by: GitHub |
DOI:10.1111/j.2041-210X.2011.00169.x | Available for download, Acknowledgement requested | OMICS_12499 | https://github.com/liamrevell/phytools, https://sources.debian.org/src/r-cran-phytools/ | SCR_015502 | 2026-09-19 12:59:25 | 718 | |||||||
|
lme4 Resource Report Resource Website 100+ mentions |
lme4 (RRID:SCR_015654) | software resource, source code | Software R package. Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue." | linear mixed-effects model, s4 class, eigen c++ library, r package, r, bio.tools |
is listed by: CRAN is listed by: bio.tools is listed by: Debian works with: R package: lmerTest |
Free, Available for download | biotools:lme4 | https://cran.r-project.org/package=lme4, https://github.com/lme4/lme4/, https://bio.tools/lme4 | SCR_015654 | lme4, lme4.0, lme4: Linear Mixed-Effects Models using 'Eigen' and S4, lme4: Linear Mixed-Effects Models, R package: lme4 | 2026-09-19 12:59:26 | 411 | |||||||
|
EvidenceFinder Resource Report Resource Website 1+ mentions |
EvidenceFinder (RRID:SCR_013764) | software resource, web application | A web application to assist in the identification of articles and research related to literature search terms. The search covers full text articles in the Europe PMC repository. Relevant papers are suggested to users based on the scientific term searched and the selection of questions, generated by the application, relevant to term searched. | web application, software resource, literature search, bio.tools |
is used by: Europe PubMed Central is listed by: Debian is listed by: bio.tools is listed by: Connected Researchers is related to: Europe PubMed Central has parent organization: Europe PubMed Central |
Wellcome Trust 098231 | DOI:10.1093/nar/gku1061 | Free, Public | biotools:evidence_finder | https://bio.tools/evidence_finder | SCR_013764 | 2026-09-19 12:55:27 | 3 | ||||||
|
MRIcron Resource Report Resource Website 1000+ mentions |
MRIcron (RRID:SCR_002403) | MRIcron | data processing software, data visualization software, software application, software resource | Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron. | NIfTI, format, image, viewer, exporting, brain, image, processing, data, bio.tools |
is used by: XFSL: An FSL toolbox is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: neurodebian is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Colour maps for brain imaging has parent organization: University of South Carolina; South Carolina; USA |
PMID:17583985 PMID:11568431 |
BSD License | biotools:MRIcron, nif-0000-00122 | https://sources.debian.org/src/mricron/, http://www.mccauslandcenter.sc.edu/mricro/, http://www.nitrc.org/projects/mricron, http://neuro.debian.net/pkgs/mricron.html, https://bio.tools/MRIcron | SCR_002403 | mricron - magnetic resonance image conversion viewing and analysis | 2026-09-19 12:55:30 | 2312 | |||||
|
IgDiscover Resource Report Resource Website 10+ mentions |
IgDiscover (RRID:SCR_024037) | data analysis software, data processing software, software application, software resource | Software to analyze antibody repertoires and discover new V genes from high-throughput sequencing reads.Heavy chains, kappa and lambda light chains are supported (to discover VH, VK and VL genes)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | analyze antibody repertoires, discover new V genes, high-throughput sequencing reads, | is listed by: Debian | PMID:27995928 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_16456 | https://sources.debian.org/src/igdiscover/, https://github.com/NBISweden/IgDiscover/ | SCR_024037 | igdiscover | 2026-09-19 12:55:41 | 11 | ||||||
|
caftools Resource Report Resource Website |
caftools (RRID:SCR_023982) | software resource | Software tools for manipulating Common Assembly Format files text format for describing sequence assemblies,that can be downloaded from the Sanger ftp site. | is listed by: Debian | Free, Available for download, Freely available | OMICS_24974 | https://sources.debian.org/src/caftools/ | SCR_023982 | 2026-09-19 12:55:40 | 0 |
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