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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Lifebit Deploit Resource Report Resource Website 1+ mentions |
Lifebit Deploit (RRID:SCR_016428) | data analysis service, analysis service resource, data management software, software resource, software application, production service resource, service resource | Platform for computing management for data analysis on the cloud from the Lifebit company. Allows the computational analyses to be permanently linked to live analyses pipelines. | Lifebit, compute, management, data, analysis, cloud, integrate, data, reproduce, transparent, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:28398311 | Commercially available | biotools:nextflow | https://bio.tools/nextflow | SCR_016428 | 2026-08-04 09:43:53 | 2 | |||||||
|
Microscopy Image Browser Resource Report Resource Website 100+ mentions |
Microscopy Image Browser (RRID:SCR_016560) | MIB | data processing software, data analysis software, standalone software, software resource, software application, image processing software, data visualization software | Software package for advanced image processing, analysis, segmentation and visualization of multi-dimensional (2D-4D) light and electron microscopy datasets. | segmentation, analysis, multidimentional, dataset, light, electron, microscopy, image, processing, visualization, data, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: MATLAB |
Biocenter Finland ; Biological Imaging Network Academy of Finland ; University of Helsinki |
PMID:26727152 | Free, Available for download, Freely available | biotools:mib | https://www.youtube.com/watch?v=I9FWmJX_nl0&index=1&list=PLGkFvW985wz8cj8CWmXOFkXpvoX_HwXzj, https://bio.tools/mib | SCR_016560 | MIB, Microscopy Image Browser | 2026-08-04 09:43:55 | 143 | ||||
|
MetaCyto Resource Report Resource Website 1+ mentions |
MetaCyto (RRID:SCR_016415) | data processing software, data analysis software, software resource, software application, software toolkit | Software tool for automated meta-analysis of mass and flow cytometry data. Provides functions for preprocessing, automated gating and meta-analysis of cytometry data and collection of cytometry data from the ImmPort database. | automated, analysis, meta, flow, cytometry, data, bio.tools |
is listed by: Bioconductor is listed by: NIDDK Information Network (dkNET) is listed by: bio.tools is listed by: Debian is related to: The Immunology Database and Analysis Portal (ImmPort) |
the National Institute of Allergy and Infectious Diseases HHSN272201200028C | Free, Available for download, Freely available | biotools:metacyto | https://bio.tools/metacyto | SCR_016415 | 2026-08-04 09:43:54 | 5 | |||||||
|
DINIES Resource Report Resource Website 1+ mentions |
DINIES (RRID:SCR_016505) | DINIES | data processing software, data analysis software, software resource, sequence analysis software, software application, web application | Web server for predicting unknown drug-target interaction networks from various types of biological data in the framework of supervised network inference. | predict, drug, target, interaction, network, biological, data, chemical, structure, protein, amino acid, sequence, domain, bio.tools |
is listed by: GenomeNet is listed by: Debian is listed by: bio.tools is related to: KEGG has parent organization: Kyoto University; Kyoto; Japan |
Ministry of Education ; Culture ; Sports ; Science and Technology of Japan ; the Japan Science and Technology Agency ; the Japan Society for the Promotion of Science |
PMID:24838565 | Free, Freely available | biotools:dinies | https://bio.tools/dinies | SCR_016505 | Drug target Interaction Network Inference Engine based on Supervised analysis | 2026-08-04 09:43:54 | 4 | ||||
|
MentaLiST Resource Report Resource Website 1+ mentions |
MentaLiST (RRID:SCR_016469) | data processing software, data analysis software, software resource, sequence analysis software, software application | Software for a MLST (multi-locus sequence typing) caller, based on a k-mer counting algorithm and written in the Julia language. Designed and implemented to handle large typing schemes. | next, generation, sequencing, multi, locus, sequence, typing, pathogen, surveillance, gene, identify, strain, type, housekeeping, whole, genome, sequencing, data, bacteria, genotyping, bio.tools |
is listed by: bio.tools is listed by: Debian |
Canadian Institute for Health Research ; Genome Canada ; Genome BC |
PMID:29319471 | Free, Available for download, Freely available | biotools:mentalist | https://bio.tools/mentalist | SCR_016469 | 2026-08-04 09:43:54 | 8 | ||||||
|
cisTEM Resource Report Resource Website 50+ mentions |
cisTEM (RRID:SCR_016502) | cisTEM | data processing software, software application, image processing software, software resource | Software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them. | data, processing, high, resolution, electron, cryo, macroscopy, single, particle, averaging, image, macromolecule, high, resolution, 3D, bio.tools |
is listed by: bio.tools is listed by: Debian |
Howard Hughes Medical Institute | DOI:10.7554/eLife.35383 | Open source, Trial available | biotools:cistem | https://bio.tools/cistem | SCR_016502 | computational imaging system for Transmission Electron Microscopy | 2026-08-04 09:43:54 | 64 | ||||
|
Pavian Resource Report Resource Website 10+ mentions |
Pavian (RRID:SCR_016679) | data analysis service, analysis service resource, software resource, production service resource, service resource, web application | Software R package for interactive analysis of metagenomics classification results with a special focus on infectious disease diagnosis. Used for analyzing and visualization of metagenomics classification results from classifiers such as Kraken, Centrifuge and MetaPhlAn. Provides an alignment viewer for validation of matches to a particular genome. | interactive, analysis, metagenomics, classification, result, infectious, disease, diagnosis, data, visualization, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Centrifuge Classifier |
NHGRI R01 HG006677; NIGMS R01 GM083873; U. S. Army Research Office W911NF1410490 |
DOI:10.1101/084715 | Free, Freely available | biotools:pavian | https://fbreitwieser.shinyapps.io/pavian/, https://bio.tools/pavian | SCR_016679 | 2026-08-04 09:43:58 | 22 | ||||||
|
Centrifuge Classifier Resource Report Resource Website 1+ mentions |
Centrifuge Classifier (RRID:SCR_016665) | data processing software, data analysis software, software resource, sequence analysis software, software application | Software for rapid and sensitive classification of metagenomic sequences. Used for the classification of DNA sequences from microbial samples and analysis of large metagenomics data sets on conventional desktop computers. | classification, large, metagenomic, sequence, DNA, microbial, sample, analysis, data, desktop, computer, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is related to: Pavian has parent organization: Center for Computational Biology at JHU |
U. S. Army Research Office W911NF1410490; NSF ABI1356078; NHGRI R01 HG006677; NIGMS R01 GM083873 |
DOI:10.1101/gr.210641.116 | Free, Available for download, Freely available | biotools:centrifuge, OMICS_12217 | https://github.com/infphilo/centrifuge, https://bio.tools/centrifuge, https://sources.debian.org/src/centrifuge/ | SCR_016665 | 2026-08-04 09:43:59 | 9 | ||||||
|
TB PORTALS Resource Report Resource Website 10+ mentions |
TB PORTALS (RRID:SCR_016594) | portal, topical portal, storage service resource, disease-related portal, consortium, organization portal, data repository, service resource, data or information resource | Web based open access platform for global drug resistant tuberculosis data sharing and analysis. The NIAID TB Portals program and consortium of clinicians and scientists from countries with a heavy burden of TB, especially drug resistant TB, to collect TB data. | collect, data, sharing, analysis, tuberculosis, global, bio.tools |
is listed by: NIAID is listed by: bio.tools is listed by: Debian |
tuberculosis | NIH | DOI:10.1128/JCM.01013-17 | Free, Freely available | r3d100013925, biotools:TB_Portals | https://bio.tools/TB_Portals, https://doi.org/10.17616/R31NJN8L | SCR_016594 | 2026-08-04 09:43:56 | 12 | |||||
|
NMRProcFlow Resource Report Resource Website 10+ mentions |
NMRProcFlow (RRID:SCR_016592) | data processing software, software application, data visualization software, software resource | Software as graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics. | NMR, metabolomics, data, viewer, spectra, processing, graphical, interface, bio.tools |
uses: R Project for Statistical Computing is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
French National Infrastructure in Metabolomics and Fluxomics | DOI:10.1007/s11306-017-1178-y | Free, Available for download, Freely available | biotools:nmrprocflow, SCR_022777 | https://github.com/INRA/NMRProcFlow, https://bio.tools/nmrprocflow, https://github.com/inra/nmrprocflow | SCR_016592 | Nuclear Magnetic Resonance PROcessing FLOW, Nuclear Magnetic Resonance Processing Flow | 2026-08-04 09:43:56 | 23 | |||||
|
CheckM Resource Report Resource Website 100+ mentions |
CheckM (RRID:SCR_016646) | data processing software, data analysis software, software resource, software application, software toolkit | Software tool to assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes by using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. | assess, quality, microbial, genome, recovered, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/gr.186072.114 | Free, Available for download, Freely available | biotools:checkm | https://github.com/Ecogenomics/CheckM, https://bio.tools/checkm | SCR_016646 | 2026-08-04 09:43:57 | 184 | |||||||
|
Genotyping Resource Report Resource Website 10+ mentions |
Genotyping (RRID:SCR_016645) | data processing software, data analysis software, web service, software resource, sequence analysis software, software application, data access protocol | Web tool to identify the genotype of a viral sequence. A window is slid along the query sequence and each window is compared by BLAST to each of the reference sequences for a particular virus. | identify, genotype, viral, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: NCBI works with: NCBI BLAST |
Free, Freely available | biotools:ncbi_genotyping | https://bio.tools/ncbi_genotyping | SCR_016645 | 2026-08-04 09:43:57 | 31 | ||||||||
|
Libra Resource Report Resource Website |
Libra (RRID:SCR_016608) | data processing software, data analysis software, software resource, sequence analysis software, software application, data analytics software | Hadoop based tool for massive comparative metagenomics analysis. Compute the similarity between metagenomic samples. | gene, distance, matrix, computation, k-mer-based, sequence, comparison, Hadoop, metagenomic, sample, bio.tools |
is listed by: bio.tools is listed by: Debian |
NSF 1640775 | Free, Available for download, Freely available | biotools:Libra_k-mer | https://bio.tools/Libra_k-mer | SCR_016608 | 2026-08-04 09:43:58 | 0 | |||||||
|
KAT Resource Report Resource Website 10+ mentions |
KAT (RRID:SCR_016741) | KAT | data processing software, data analysis software, software resource, software application, software toolkit | Software that generates, analyses and compares k-mer spectra produced from sequence files. Used to quality control NGS datasets and genome assemblies. | generate, analyse, compare, k-mer, spectra, sequence, file, quality, control, NGS, dataset, genome, assembly, bio.tools |
is listed by: Debian is listed by: bio.tools |
BBSRC | DOI:10.1093/bioinformatics/btw663 | Free, Available for download, Freely available | biotools:kat | http://www.earlham.ac.uk/kat-tools, https://bio.tools/kat | SCR_016741 | K-mer Analysis Toolkit | 2026-08-04 09:44:00 | 19 | ||||
|
kallisto Resource Report Resource Website 100+ mentions |
kallisto (RRID:SCR_016582) | data processing software, software application, software resource, data analysis software | Software tool for quantifying abundances of transcripts from RNA-Seq data or target sequences using high-throughput sequencing reads. | bio.tools |
is listed by: Debian is listed by: bio.tools works with: sleuth works with: kb_python |
PMID:27043002 | Free, Available for download, Freely available | biotools:kallisto | https://pachterlab.github.io/kallisto/download.html, https://bio.tools/kallisto, https://sources.debian.org/src/kallisto/ | SCR_016582 | kallisto v0.43.1 | 2026-08-04 09:43:56 | 127 | ||||||
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rCASC Resource Report Resource Website 1+ mentions |
rCASC (RRID:SCR_017005) | data processing software, software application, software resource, data analysis software | Software package for reproducible classification analysis of single cell sequencing data. | reproducibility, classification, analysis, single, cell, sequencing, data, bio.tools |
is used by: Stardust is listed by: Debian is listed by: bio.tools is related to: University of Turin;Turin;Italy |
PMID:24204232 | Free, Available for download, Freely available | biotools:rCASC | https://kendomaniac.github.io/rCASC/, https://bio.tools/rCASC | SCR_017005 | rCASC, reproducible Cluster Analysis of Single Cells | 2026-08-04 09:44:02 | 1 | ||||||
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Flye Resource Report Resource Website 100+ mentions |
Flye (RRID:SCR_017016) | data processing software, data analysis software, software resource, sequence analysis software, software application, software toolkit | Software package as de novo assembler for single molecule sequencing reads. Used for assembling long, error prone reads such as those produced by PacBio and Oxford Nanopore Technologies, for fast and accurate genome reconstructions. Available for Linux and MacOS platforms. | assembler, single, molecule, sequencing, long, error, read, fast, accurate, genome, reconstruction, nucleotide, quality, data, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of California at San Diego; California; USA |
PMID:27956617 | Free, Available for download, Freely available | biotools:Flye | https://bio.tools/Flye, https://sources.debian.org/src/flye/ | SCR_017016 | 2026-08-04 09:44:03 | 267 | |||||||
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CCTOP Resource Report Resource Website 10+ mentions |
CCTOP (RRID:SCR_016963) | CCTOP | analysis service resource, web service, software resource, data access protocol, production service resource, service resource | Web application providing transmembrane topology prediction. Server incorporates topology information from existing experimental and computational sources using the probabilistic framework of hidden Markov model. Provides the option to precede the topology prediction with signal peptide prediction and transmembrane globular protein discrimination. Given the amino acid sequence of a putative α helical transmembrane protein, CCTOP predicts its topology i.e. localization of membrane spanning regions and orientation of segments between them. | transmembrane, topology, prediction, signal, peptide, globular, protein, discrimination, amino, acid, sequence, region, orientation, segment, bio.tools |
is listed by: Debian is listed by: bio.tools works with: PDBTM works with: Topology Data Bank of Transmembrane Proteins works with: TopDom |
Hungarian Scientific Research Fund | PMID:25943549 | Free, Freely available | biotools:cctop | https://bio.tools/cctop | SCR_016963 | CCTOP, Consensus Constrained TOPology | 2026-08-04 09:44:01 | 29 | ||||
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Illuminating the Druggable Genome Resource Report Resource Website 10+ mentions |
Illuminating the Druggable Genome (RRID:SCR_016924) | IDG | portal, storage service resource, consortium, organization portal, data repository, service resource, data or information resource | Program to improve understanding of properties and functions of proteins that are currently unannotated within three most commonly drug protein families: targeted G-protein coupled receptors, ion channels, and protein kinases. Includes Data and Resource Generating Centers (DRGC), Knowledge Management Center (KMC), and Resource Dissemination and Outreach Center (RDOC). | understudied, target, protein, G protein, coupled, receptor, ion, channel, kinase, bio.tools |
is recommended by: National Library of Medicine is listed by: NIDDK Information Network (dkNET) is listed by: bio.tools is listed by: Debian |
NIH Common Fund | biotools:pharos | https://pharos.nih.gov/, https://bio.tools/pharos, https://darkmatter.ucsf.edu/about | https://druggablegenome.net | SCR_016924 | Pharos, Illuminating the Druggable Genome, IDG, Illuminating Druggable Genome | 2026-08-04 09:44:01 | 45 | |||||
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Thunder STORM Resource Report Resource Website 10+ mentions |
Thunder STORM (RRID:SCR_016897) | ThunderSTORM | data processing software, data analysis software, software resource, software application, software toolkit | Software tool for automated processing, analysis, and visualization of data acquired by single molecule localization microscopy methods such as PALM and STORM. ImageJ interactive and modular plugin for SMLM data analysis and super-resolution imaging. | automated, processing, analysis, visualization, data, acquired, single, molecule, localization, microscopy, SMLM, imaging, bio.tools |
is listed by: Debian is listed by: bio.tools is a plug in for: ImageJ |
Czech Science Foundation ; Charles University ; European Regional Development Fund ; European Social Fund |
PMID:24771516 | Free, Available for download, Freely available | biotools:thunderstorm | https://bio.tools/thunderstorm | SCR_016897 | 2026-08-04 09:44:00 | 42 |
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