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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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VisR Resource Report Resource Website 1+ mentions |
VisR (RRID:SCR_016658) | VisR | data processing software, data analysis software, software resource, software application, data visualization software, software toolkit | Software as an R-based visual framework for analysis of sequencing datasets. Provides a framework for integrative and interactive analyses. | visual, framework, analysis, sequencing, data, dataset, integrative, interactive, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Bioconductor |
Michael Smith Foundation for Health Research ; Canadian Institutes of Health Research (CIHR) and Genome BC ; NSERC PGS-D |
PMID:26328469 | Free, Available for download, Freely available | biotools:VisR | https://bio.tools/VisR | SCR_016658 | VisRseq, VisR | 2026-08-04 09:43:58 | 5 | ||||
|
IndelGenotyper Resource Report Resource Website 50+ mentions |
IndelGenotyper (RRID:SCR_016663) | GATK | data processing software, data analysis software, software resource, sequence analysis software, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18th,2023. Software package for genome analysis. Used for analysis of next generation genomic data in cancer. | next, generation, analysis, genomic, data, cancer, genome |
is listed by: Debian has parent organization: Broad Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/broadinstitute/gatk/, https://sources.debian.org/src/gatk/ | SCR_016663 | GATK Indel Genotyper, Genome Analysis Toolkit (GATK) Indel Genotyper, Indel Genotyper, GATK IndelGenotyper | 2026-08-04 09:43:57 | 63 | |||||||
|
biobakery Resource Report Resource Website 10+ mentions |
biobakery (RRID:SCR_016596) | data processing software, data analysis software, software resource, software application, 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 |
NIDDK U54 DE023798; Sloan Foundation 4406J0B; NHGRI R01 HG005220; NSF DBI1053486; NHGRI R01 HG005969; ARO W911NF1110473 |
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 | 2026-08-04 09:43:57 | 13 | |||||
|
Discovar assembler Resource Report Resource Website 10+ mentions |
Discovar assembler (RRID:SCR_016755) | Discovar | data processing software, data analysis software, software resource, sequence analysis software, software application | Software tool for variant calling with reference and de novo assembly of genomes. The heart of DISCOVAR is a de novo genome assembler which can generate de novo assemblies for both large and small genomes. | variant, calling, reference, de novo, assembly, genome, genetic, human, sequence, analysis |
is listed by: OMICtools has parent organization: Broad Institute |
NHGRI R01 HG003474; NHGRI U54 HG003067; NIAID HHSN272200900018C |
PMID:25326702 | Free, Available for download, Freely available | SCR_016755 | Discovar de novo, Discovar | 2026-08-04 09:43:59 | 20 | ||||||
|
rsfMRI_fconn calculation Resource Report Resource Website 1+ mentions |
rsfMRI_fconn calculation (RRID:SCR_016591) | rsfMRI_fconn calculation | data processing software, software application, software resource, data analysis software | 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 | 2026-08-04 09:43:56 | 1 | |||||||||
|
PhenoMeNal Resource Report Resource Website 1+ mentions |
PhenoMeNal (RRID:SCR_016605) | phnmnl, PhenoMeNal | portal, web service, software resource, consortium, data access protocol, organization portal, data or information resource | 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 | 2026-08-04 09:43:57 | 2 | |||||
|
SPICE Resource Report Resource Website 50+ mentions |
SPICE (RRID:SCR_016603) | SPICE | data processing software, data analysis software, software resource, software application, data visualization software | 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 | 2026-08-04 09:43:56 | 66 | ||||
|
JOINSOLVER Resource Report Resource Website |
JOINSOLVER (RRID:SCR_016619) | data processing software, alignment software, data analysis software, software resource, software application, image analysis software, service 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 | 2026-08-04 09:43:57 | 0 | ||||||||
|
Simmune Resource Report Resource Website 1+ mentions |
Simmune (RRID:SCR_016618) | Simmune | data processing software, data analysis software, software resource, software application, 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 | 2026-08-04 09:43:57 | 1 | ||||||||
|
SPM U+ Resource Report Resource Website 1+ mentions |
SPM U+ (RRID:SCR_016743) | SPM U+ | data processing software, data analysis software, software resource, software application, 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+ | 2026-08-04 09:43:59 | 4 | ||||||||
|
riboSeqR Resource Report Resource Website 1+ mentions |
riboSeqR (RRID:SCR_016947) | data processing software, software application, software resource, data analysis software | 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 | 2026-08-04 09:44:01 | 4 | ||||||||||
|
Rsubread Resource Report Resource Website 100+ mentions |
Rsubread (RRID:SCR_016945) | data processing software, alignment software, data analysis software, software resource, software application, image analysis software | 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 National Health and Medical Research Council ; Victorian State Government Operational Infrastructure Support ; Australian Government |
PMID:23558742 | Free, Available for download, Freely available | biotools:rsubread | https://bio.tools/rsubread | SCR_016945 | 2026-08-04 09:44:01 | 188 | ||||||
|
scran Resource Report Resource Website 50+ mentions |
scran (RRID:SCR_016944) | SCRAN | data processing software, software application, software resource, data analysis software | 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 ; National Health and Medical Research Council of Australia ; EMBL |
PMID:27909575 | Free, Available for download, Freely available | biotools:scran | https://bio.tools/scran | SCR_016944 | Single-Cell Rna-seq data ANalysis, SCRAN | 2026-08-04 09:44:02 | 92 | ||||
|
ConsensusClusterPlus Resource Report Resource Website 100+ mentions |
ConsensusClusterPlus (RRID:SCR_016954) | data processing software, software application, software resource, data analysis software | 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; Thomas G. Labrecque Foundation ; NCI U24 CA126554 |
PMID:20427518 | Free, Available for download, Freely available | biotools:consensusclusterplus | https://bio.tools/consensusclusterplus | SCR_016954 | 2026-08-04 09:44:03 | 160 | ||||||
|
Bulked segregation analysis tools for outbreeding species Resource Report Resource Website 1+ mentions |
Bulked segregation analysis tools for outbreeding species (RRID:SCR_017009) | BSATOS | data processing software, data analysis software, time-series analysis software, software resource, software application, 1d time-series analysis software | Software tools for next generation sequencing based bulked segregation analysis for outbreeding species including fruit trees such as apple or cirtus. Used to improve gene mapping efficiency of next generation sequencing based segregant analysis in outbreeding species and realize rapid candidate gene mining based on multi-omics data. | next, generation, sequencing, bulked, segregation, analysis, outbreeting, specie, gene, mapping, data | Free, Available for download, Freely available | SCR_017009 | Bulked segregation analysis tools for outbreeding species, Bulked Segregation Analysis Tools for Outbreeding Species, BSATOS | 2026-08-04 09:44:02 | 2 | |||||||||
|
Motion Sensing Superpixels (MOSES) Resource Report Resource Website 1+ mentions |
Motion Sensing Superpixels (MOSES) (RRID:SCR_016839) | MOSES | data processing software, software application, software resource, data analysis software | 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 | 2026-08-04 09:43:59 | 1 | ||||||||
|
GenomeScope Resource Report Resource Website 500+ mentions |
GenomeScope (RRID:SCR_017014) | Genomescope | data processing software, data analysis software, software resource, software application, service resource | Open source software package for fast genome analysis from unassembled short reads. Used to estimate genome heterozygosity, repeat content, and size from sequencing reads using a kmer-based statistical approach. | genome, unassembled, sequenced, data, short, read, analysis, heterozygosity, repeat, content, size, kmer | is related to: Cold Spring Harbor Laboratory | NSF DBI 1350041; NSF IOS 1237880; NHGRI R01 HG006677 |
PMID:28369201 | Free, Freely available, | http://qb.cshl.edu/genomescope/ | SCR_017014 | 2026-08-04 09:44:04 | 651 | ||||||
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OptiQuant Software Resource Report Resource Website 1+ mentions |
OptiQuant Software (RRID:SCR_016769) | image acquisition software, data processing software, data analysis software, software resource, software application, image analysis software, data acquisition software | 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 | 2026-08-04 09:43:59 | 4 | |||||||||
|
mixOmics Resource Report Resource Website 50+ mentions |
mixOmics (RRID:SCR_016889) | data processing software, software application, software resource, data analysis software | 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 | 2026-08-04 09:44:00 | 58 | ||||||||||
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BISE Resource Report Resource Website 10+ mentions |
BISE (RRID:SCR_016774) | portal, analysis service resource, software resource, organization portal, production service resource, service resource, database, data or information 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 | 2026-08-04 09:43:59 | 12 |
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