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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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biobakery Resource Report Resource Website 10+ mentions |
biobakery (RRID:SCR_016596) | data analysis software, data processing software, software application, software resource, software toolkit | Analysis environment and collection of individual software tools to process raw shotgun metagenome or metatranscriptome sequencing data for quantitative microbial community profiling. Used for a metaomics data analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Huttenhower lab, metaomics, data, analysis, process, raw, shotgun, metagenome, metatranscriptome, sequencing, microbial, profiling, bio.tools |
is used by: Nephele is listed by: Debian is listed by: bio.tools is related to: Human Microbiome Project has parent organization: Harvard University; Cambridge; United States |
ARO W911NF1110473; NHGRI R01 HG005220; NHGRI R01 HG005969; NIDDK U54 DE023798; NSF DBI1053486; Sloan Foundation 4406J0B |
PMID:29194469 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:biobakery | http://huttenhower.sph.harvard.edu/biobakery, https://bio.tools/biobakery | SCR_016596 | bioBakery, biobakery | 2026-09-12 12:58:42 | 18 | |||||
|
rsfMRI_fconn calculation Resource Report Resource Website 1+ mentions |
rsfMRI_fconn calculation (RRID:SCR_016591) | rsfMRI_fconn calculation | data analysis software, data processing software, software application, software resource | Software program for preprocessing resting state functional magnetic resonance imaging (rsfMRI) measurements and calculating region of interest based whole brain functional connectivity. | data, resting, state, brain, processing, functional, magnetic, resonance, imaging, measurement, calculate, region, connectivity, analysis, sequence |
uses: SPM is related to: MATLAB |
SCR_016591 | resting state functional MRI and functional connectivity calculation, resting state functional MRI pre processing and Functional Connectivity calculation | 2026-09-12 12:58:42 | 1 | |||||||||
|
PhenoMeNal Resource Report Resource Website 1+ mentions |
PhenoMeNal (RRID:SCR_016605) | phnmnl, PhenoMeNal | consortium, data access protocol, data or information resource, organization portal, portal, software resource, web service | Cloud based standardised European e-infrastructure for metabolomics and phenomics data processing, analysis and information mining on public or private cloud providers. Used for large scale computing for medical metabolomics. | metabolomic, phenomic, data, processing, analysis, information, mining. medical, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: European Molecular Biology Laboratory has parent organization: European Bioinformatics Institute |
European Commission EC654241 | Free, Registration required, Tutorial available | biotools:PhenoMeNal | https://github.com/phnmnl, https://bio.tools/PhenoMeNal | SCR_016605 | Phenome and Metabolome aNalysis | 2026-09-12 12:58:42 | 3 | |||||
|
SPICE Resource Report Resource Website 50+ mentions |
SPICE (RRID:SCR_016603) | SPICE | data analysis software, data processing software, data visualization software, software application, software resource | Software application for data mining and visualization. Used for analyzes of large FLOWJO data sets from polychromatic flow cytometry and organizing the normalized data graphically. | data, mining, visualization, analysis, polychromatic, flow, cytometry, dataset, normalized, graphically, bio.tools |
is listed by: NIAID is listed by: Debian is listed by: bio.tools |
NIAID ; NIH |
PMID:21265010 | Free, Available for download, Freely available | biotools:spice | https://bio.tools/spice | SCR_016603 | Simplified Presentation of Incredibly Complex Evaluations | 2026-09-12 12:58:42 | 72 | ||||
|
JOINSOLVER Resource Report Resource Website |
JOINSOLVER (RRID:SCR_016619) | alignment software, data analysis software, data processing software, image analysis software, service resource, software application, software resource | Software tool to analyze human immunoglobulin V(D)J recombination and performing Ig nucleotide and amino acid alignment, as well as extensive mutation and Complementarity Determining Region 3 (CDR3H) analysis. | human, immunoglobulin, analysis, recombination, nucleotide, amino acid, alignment, mutation, CDR3H |
is listed by: NIDDK Information Network (dkNET) is listed by: NIAID |
DOI:10.4049/jimmunol.172.11.6790 | Free, Available for download, Freely available | https://dcb.cit.nih.gov/HTJoinSolver/ | SCR_016619 | 2026-09-12 12:58:42 | 0 | ||||||||
|
Simmune Resource Report Resource Website 1+ mentions |
Simmune (RRID:SCR_016618) | Simmune | data analysis software, data processing software, software application, software resource, software toolkit | Software package to define the interactions between individual molecules in a large network or the behaviors of cells in response to external signals. It consists of three components: Modeler, Cell Designer and Simulator. | interaction, analysis, molecule, network, cell, response, external, signal |
is listed by: NIDDK Information Network (dkNET) has parent organization: University of Hamburg; Hamburg; Germany |
Free, Available for download, Freely available | SCR_016618 | simulate immunological phenomena | 2026-09-12 12:58:42 | 1 | ||||||||
|
SPM U+ Resource Report Resource Website 1+ mentions |
SPM U+ (RRID:SCR_016743) | SPM U+ | data analysis software, data processing software, software application, software resource, software toolkit | Software Project Management (SPM) tools which contain a collection of functions that can be used at different stage of a standard massive univariate fMRI data analysis. Used to improve mass univariate analysis. | SPM, standard, massive, univariate, plus, data, fMRI, analysis | Free, Available for download, Freely available | https://osf.io/wn3h8/ | SCR_016743 | , Software Project Management Univariate Plus, SPM Univariate Plus, SPM U+, Software Project Management U+ | 2026-09-12 12:58:44 | 5 | ||||||||
|
riboSeqR Resource Report Resource Website 1+ mentions |
riboSeqR (RRID:SCR_016947) | data analysis software, data processing software, software application, software resource | Software tool for analysis of sequencing data from ribosome profiling experiments. Used for plotting functions, frameshift detection and parsing of sequencing data from ribosome profiling experiments. | analysis, sequencing, data, ribosome, profiling, experiment, plotting, function, frameshift, detect, parsing |
is listed by: Bioconductor is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_016947 | 2026-09-12 12:58:46 | 4 | ||||||||||
|
Rsubread Resource Report Resource Website 100+ mentions |
Rsubread (RRID:SCR_016945) | alignment software, data analysis software, data processing software, image analysis software, software application, software resource | Software R package for sequence alignment and counting for R. Used for analyses of second and third generation sequencing data, for read mapping, read counting, SNP calling, short and long read alignment, quantification and mutation discovery. Includes assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. Can be used with reads generated from any of the major sequencing platforms including Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers. | sequence, alignment, counting, multi, seed, strategy, mapping, read, reference, genome, analysis, data, SNP, calling, mutation, discovery, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing is related to: Subread |
Australian Government ; Australian National Health and Medical Research Council ; Victorian State Government Operational Infrastructure Support |
PMID:23558742 | Free, Available for download, Freely available | biotools:rsubread | https://bio.tools/rsubread | SCR_016945 | 2026-09-12 12:58:46 | 203 | ||||||
|
scran Resource Report Resource Website 100+ mentions |
scran (RRID:SCR_016944) | SCRAN | data analysis software, data processing software, software application, software resource | Software package for low-level analyses of single-cell RNA-seq data. Used for quality control, data exploration and normalization, cell cycle phase assignment, identification of highly variable and correlated genes, clustering into subpopulations and marker gene detection. | low, level, analysis, scRNA-seq, data, normalization, cell, cycle, phase, gene, variable, correlation, cluster, subpopulation, marker, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
Cancer Research UK ; EMBL ; National Health and Medical Research Council of Australia |
PMID:27909575 | Free, Available for download, Freely available | biotools:scran | https://bio.tools/scran | SCR_016944 | Single-Cell Rna-seq data ANalysis, SCRAN | 2026-09-12 12:58:46 | 100 | ||||
|
ConsensusClusterPlus Resource Report Resource Website 100+ mentions |
ConsensusClusterPlus (RRID:SCR_016954) | data analysis software, data processing software, software application, software resource | Software written in R for determining cluster count and membership by stability evidence in unsupervised analysis. Provides quantitative and visual stability evidence for estimating the number of unsupervised classes in a dataset with item tracking, item consensus and cluster consensus plots. | cluster, count, stability, evidence, unsupervised, analysis, , bio.tools |
is listed by: Bioconductor is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
NCI F32CA142039; NCI U24 CA126554; Thomas G. Labrecque Foundation |
PMID:20427518 | Free, Available for download, Freely available | biotools:consensusclusterplus | https://bio.tools/consensusclusterplus | SCR_016954 | 2026-09-12 12:58:46 | 196 | ||||||
|
Motion Sensing Superpixels (MOSES) Resource Report Resource Website 1+ mentions |
Motion Sensing Superpixels (MOSES) (RRID:SCR_016839) | MOSES | data analysis software, data processing software, software application, software resource | Computational Python library for the motion analysis of biological single-cell and collective motion for high content screens. Framework to quantify and discover cellular motion phenotypes. | motion, analysis, biological, single, cell, collective, motion, high, content, screen, quantify, discover, phenotype | DOI:10.1101/248104 | Free, Freely available for academic non commercial research | SCR_016839 | Motion Sensing Superpixels (MOSES), MOSES, Motion Sensing Superpixels | 2026-09-12 12:58:44 | 1 | ||||||||
|
OptiQuant Software Resource Report Resource Website 1+ mentions |
OptiQuant Software (RRID:SCR_016769) | data acquisition software, data analysis software, data processing software, image acquisition software, image analysis software, software application, software resource | Software package for image acquisition, analysis, display, and archiving. Used to quantify the autoradiography data from Cyclone apparatus from Perkin Elmer. | image, acquisition, analysis, display, archiving, quantify, autoradiography, data, PerkinElmer | Commercially available, Free download available | https://optiquant.software.informer.com/5.0/ | SCR_016769 | OptiQuant, OptiQuant 3.0, OptiQuant software 5.0, OptiQuant 5.0 | 2026-09-12 12:58:44 | 4 | |||||||||
|
mixOmics Resource Report Resource Website 50+ mentions |
mixOmics (RRID:SCR_016889) | data analysis software, data processing software, software application, software resource | Software R package of multivariate methods for the exploration and integration of biological datasets with a focus on variable selection. Used to analyse data from high throughput sequencing technologies and spectral imaging., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | multivariate, exploration, integration, biological, dataset, variable, selection, analysis, data, high, throughput, sequencing, technology, spectral, imaging |
is related to: R Project for Statistical Computing has parent organization: University of Melbourne; Victoria; Australia |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016889 | 2026-09-12 12:58:45 | 61 | ||||||||||
|
BISE Resource Report Resource Website 10+ mentions |
BISE (RRID:SCR_016774) | analysis service resource, data or information resource, database, organization portal, portal, production service resource, service resource, software resource | Web platform for bio image analysis. Used to share knowledge between the different communities, to help biologists to find any tool or workflow available for a particular image analysis problem and to find the adequate image processing wording, to help software and algorithm developers to find missing tools (or components), and to help bioimage analyst to identify and edit workflows. | bioimage, analysis, data, information, image, processing, algorithm, workflow, bio.tools |
lists: FibrilTool is listed by: Debian is listed by: bio.tools has parent organization: NEUBIAS |
Free, Freely available, Registration required | biotools:BISE | https://bio.tools/BISE | SCR_016774 | 2026-09-12 12:58:44 | 13 | ||||||||
|
Tools for NIfTI and ANALYZE image Resource Report Resource Website 1+ mentions |
Tools for NIfTI and ANALYZE image (RRID:SCR_016895) | data analysis software, data processing software, image analysis software, service resource, software application, software resource, software toolkit | Matlab based scripts for load, save, make, reslice, view and edit both Neuroimaging Informatics Technology Initiative (NIfTI) and ANALYZE data on any platform. | neuroimaging, data, program, analysis, image |
is related to: NIfTI Data Format Working Group is related to: MATLAB |
Free, Available for download, Freely available | https://perso.telecom-paristech.fr/bloch/P6Image/Projets/Nez2/NIfTI_matlab_tools/NIfTI_tools.pdf | SCR_016895 | Neuroimaging Informatics Technology Initiative (NIfTI) and Analyze Image data | 2026-09-12 12:58:45 | 1 | ||||||||
|
FlowSOM Resource Report Resource Website 100+ mentions |
FlowSOM (RRID:SCR_016899) | data analysis software, data processing software, data visualization software, software application, software resource | Software tool to analyze Flow or mass cytometry data using a Self-Organizing Map. Used to obtain an overview of how all markers are behaving on all cells, and to detect subsets that might be missed otherwise. | flow, cytometry, data, analysis, self, organizing, map, marker, cell, detect, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is related to: R Project for Statistical Computing is a plug in for: FlowJo |
PMID:25573116 | Free, Available for download, Freely available | biotools:flowsom | https://bioconductor.org/packages/release/bioc/html/FlowSOM.html, https://www.flowjo.com/exchange/#/plugin/profile?id=7, https://bio.tools/flowsom | SCR_016899 | FlowSOM, Flow Self Organizing Map | 2026-09-12 12:58:45 | 125 | ||||||
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CoSMoS_Analysis Resource Report Resource Website 10+ mentions |
CoSMoS_Analysis (RRID:SCR_016896) | CoSMoS Analysis | data analysis software, data processing software, image analysis software, software application, software resource | Software tools for analyzing co-localization single-molecule spectroscopy image data. | co-localization, single, molecule, spectroscopy, image, data, analysis | NIGMS ; NIH |
Free, Available for download, Freely available | SCR_016896 | co-localization single-molecule spectroscopy, Co-localization Single-Molecule Spectroscopy Analysis, co-localization single molecule spectroscopy, CoSMoS | 2026-09-12 12:58:45 | 18 | ||||||||
|
PESTO Resource Report Resource Website 10+ mentions |
PESTO (RRID:SCR_016891) | PESTO | data analysis software, data processing software, software application, software resource, software toolkit | Software customizable toolbox for parameter estimation in MathWorks MATLAB. Offers scalable algorithms for optimization, uncertainty and identifiability analysis which do not depend on any problem-specific assumptions. | parameter, estimation, MATLAB, algorithm, optimization, uncertainty, identifiability, analysis | is related to: MATLAB | European Union‘s Horizon ; German Federal Ministry of Education and Research ; German Research Foundation via the Graduate School of Quantitative Biosciences Munich |
PMID:29069312 | Free, Available for download, Freely available | https://zenodo.org/record/579890#.XDZvSlxKiM9 | SCR_016891 | Parameter EStimation TOolbox, PESTO | 2026-09-12 12:58:45 | 11 | |||||
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dcmqi Resource Report Resource Website 1+ mentions |
dcmqi (RRID:SCR_016933) | dcmqi | data processing software, image processing software, software application, software library, software resource, software toolkit | Software library to help with the conversion between imaging research formats and the standard DICOM representation for image analysis results. Used to implement conversion of the data stored in commonly used research formats into the standard DICOM representation. Available as a precompiled binary package for every major operating system, as a Docker image, and as an extension to 3D Slicer. | DICOM, converter, medical, image, computing, quantitative, analysis, clinical, data, metadata, radiology, standard, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Harvard University; Cambridge; United States |
NCI U24 CA180918; NIBIB P41 EB01589; NIBIB P41 EB015902; NIBIB R01 EB014955 |
PMID:29092948 | Free, Available for download, Freely available, Tutorial available | biotools:dcmqi | https://github.com/QIICR/dcmqi, https://bio.tools/dcmqi | SCR_016933 | DICOM for Quantitative Imaging, The Digital imaging and Communications in Medicine for Quantitative Imaging, Digital imaging and Communications in Medicine for Quantitative Imaging, DCMQI | 2026-09-12 12:58:46 | 4 |
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