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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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HeteroAnalysis Resource Report Resource Website 50+ mentions |
HeteroAnalysis (RRID:SCR_014991) | data processing software, data analysis software, algorithm resource, software resource, software application | Software for analyzing sedimentation equilibrium (SE) data from analytical ultracentrifugation experiments. It uses a model-dependent simulation of data for matching data in order to determine when equilibrium has been achieved. | sedimentation equilibrium, ultracentrifugation, analysis, model dependent | has parent organization: University of Connecticut; Connecticut; USA | Available for download | http://core.uconn.edu/files/auf/ha-help/HA-Help.htm | SCR_014991 | HeteroAnalysis Version 1.1.0.58 | 2026-08-04 09:43:33 | 62 | ||||||||
|
NetPyNE Resource Report Resource Website 10+ mentions |
NetPyNE (RRID:SCR_014758) | data processing software, data analysis software, software resource, software application, network analysis software | Software Python package for simulation and analysis of neuronal networks using the NEURON simulator.Used to facilitate development, parallel simulation, analysis, and optimization of biological neuronal networks. | Simulation, analysis, neuronal, network, NEURON, simulator, BRAIN Initiative |
uses: Python Programming Language is recommended by: BRAIN Initiative works with: NEURON |
NIBIB EB022903 | DOI:10.7554/eLife.44494.001 | Free, Available for download, Freely available | http://www.neurosimlab.org/netpyne/overview.html | SCR_014758 | Network development Python package for NEURON | 2026-08-04 09:43:32 | 26 | ||||||
|
RTCA Software Resource Report Resource Website 10+ mentions |
RTCA Software (RRID:SCR_014821) | data processing software, data analysis software, software resource, software application, data acquisition software | Data acquisition and analysis software used for xCELLigence Real Time Cell Analysis SP, DP and MP instruments. The software is used to program and execute experiments and analyze data. | system management software, cell, analysis, real time, data acquisition, data analysis | Commercially available | SCR_014821 | Real Time Cell Analysis (RTCA) Software, Real Time Cell Analysis Software, RTCA 2.0 Software | 2026-08-04 09:43:32 | 23 | ||||||||||
|
MetaboAnalyst Resource Report Resource Website 10000+ mentions |
MetaboAnalyst (RRID:SCR_015539) | data analysis service, analysis service resource, web service, software resource, data access protocol, production service resource, service resource | Web server for statistical, functional and integrative analysis of metabolomics data. Web based tool suite used for metabolomic data processing, normalization, multivariate statistical analysis, and data annotation, biomarker discovery and classification. | statistical, functional, integrative, analysis, metabolomics, data, processing, annotation, biomarker, discovery |
is listed by: SoftCite has parent organization: McGill University; Montreal; Canada has parent organization: University of Alberta; Alberta; Canada |
Alberta Ingenuity Fund ; Alberta Life Sciences Institute ; Canadian Institutes for Health Research ; Genome Alberta ; McGill University ; Natural Sciences and Engineering Research Council of Canada ; Genome Canada ; Canada Research Chairs Program |
PMID:29762782 | Free, Available for download, Freely available, Tutorial available, Acknowledgement requested | SCR_016717 | http://old.metaboanalyst.ca/MetaboAnalyst/ | SCR_015539 | MetaboAnalyst 4.0, MetaboAnalyst 3.0 | 2026-08-04 09:43:40 | 10983 | |||||
|
Ariba Resource Report Resource Website 100+ mentions |
Ariba (RRID:SCR_015976) | data processing software, data analysis software, software resource, sequence analysis software, software application, software toolkit | Analysis software that identifies antibiotic resistance genes by running local assemblies. It can also be used for MLST calling. | software, analysis, tool, sequence, antibiotic, resistance, assembly, local, mlst |
is listed by: Debian is listed by: OMICtools |
Wellcome Trust 206194; Biotechnology and Biological Sciences Research Council BB/M014088/1 |
PMID:29177089 DOI:10.1099/mgen.0.000131 |
Free, Available for download, Freely available | OMICS_17327 | https://sources.debian.org/src/artemis/ | SCR_015976 | 2026-08-04 09:43:47 | 197 | ||||||
|
Autogrid Resource Report Resource Website 1000+ mentions |
Autogrid (RRID:SCR_015982) | simulation software, data processing software, data analysis software, software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software for automated docking analysis to precalculate the set of grids describing the target protein. It is a part of automated molecular modeling simulation software AutoDock. | software, automated, docking, analysis, tool, precalculate, set, grid, ligand, protein, target, molecular, simulation, modeling, protein-ligand interaction, data |
is listed by: SoftCite is related to: AutoDock has parent organization: The Scripps Research Institute Labs and Facilities |
The Scripps Research Institute ; San Diego ; California |
PMID:16862531 | THIS RESOURCE IS NO LONGER IN SERVICE | http://mgl.scripps.edu/forum | SCR_015982 | Autogrid toolkit, Autogrid: automated grid | 2026-08-04 09:43:47 | 1146 | ||||||
|
Atac Resource Report Resource Website 1000+ mentions |
Atac (RRID:SCR_015980) | data processing software, alignment software, data analysis software, software resource, sequence analysis software, software application, image analysis software | Alignment analysis software tool for comparative mapping between two genome assemblies or between two different genomes. It can cache intermediate results to speed a comparisons of multiple sequences. | software, tool, DNA, sequence, analysis, aligning, genome, compare, mapping, assembly, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1093/bioinformatics/btr285 | Free, Freely available, Available for download | OMICS_29044, biotools:atac | https://bio.tools/atac, https://sources.debian.org/src/atac/ | SCR_015980 | 2026-08-04 09:43:47 | 1748 | |||||||
|
Axe Resource Report Resource Website 1+ mentions |
Axe (RRID:SCR_015984) | data processing software, data analysis software, software resource, sequence analysis software, software application, software toolkit | Software for sequencing data analysis and demultiplexing. It can be used in situations where sequence reads contain the barcodes that uniquely distinguish samples. | software, tool, sequence, analysis, barcode, demultiplexing |
is listed by: Debian is listed by: OMICtools |
Free, Freely available, Available for download | OMICS_19788 | https://readthedocs.org/projects/axe-demultiplexer/, https://sources.debian.org/src/baitfisher/ | SCR_015984 | Axe-demultiplexer | 2026-08-04 09:43:47 | 1 | |||||||
|
Bamtools Resource Report Resource Website 100+ mentions |
Bamtools (RRID:SCR_015987) | data processing software, data analysis software, data management software, software resource, software application, software toolkit | Software that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating genome sequence alignment files in the BAM and SAM formats. It is used for research analysis and management of data produced by sequencing technologies. | c++, api, sam, bam genome, sequence, alignment, data, analysis, management, command, manipulation, binary, map, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01 HG004719; NHGRI RC2 HG005552 |
PMID:21493652 DOI:10.1093/bioinformatics/btr174 |
biotools:bamtools, OMICS_11315 | https://bio.tools/bamtools, https://sources.debian.org/src/bamtools/ | SCR_015987 | API:Application Programming Interface, BAM:Binary Alignment Map, SAM:Sequence Alignment Map | 2026-08-04 09:43:47 | 324 | ||||||
|
MRTool Resource Report Resource Website 1+ mentions |
MRTool (RRID:SCR_015956) | topical portal, portal, data or information resource | Software toolkit for analysis of MR brain imaging data. MRTool runs on Apple computers and PCs and requires SPM12. | brain, imaging, neuroimaging, analysis, magnetic, resonance, mr | requires: SPM | DOI:10.1007/s12021-018-9355-3 | Free, Available for download, Runs on MAC OS, Runs on Windows | SCR_015956 | 2026-08-04 09:43:46 | 8 | |||||||||
|
scater Resource Report Resource Website 100+ mentions |
scater (RRID:SCR_015954) | data processing software, data analysis software, software resource, sequence analysis software, software application, data visualization software, software toolkit | Software toolkit for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control. This package facilitates pre-processing, quality control, normalization and visualization of scRNA-seq data. | scRNA-seq, rna, rnaseq, single, cell, analysis, gene, expression, quality, control, preprocessing, normalization, visualization, r, bio.tools |
is listed by: Debian is listed by: bio.tools |
National Health and Medical Research Council of Australia APP1112681; European Molecular Biology Laboratory ; Cancer Research UK A17197; United Kingdom Medical Research Council ; Oxford Single Cell Biology Consortium |
Free, Available for download | biotools:scater | https://bioconductor.org/packages/scater/, https://bio.tools/scater | SCR_015954 | scater (single-cell analysis toolkit for gene expression data in R) | 2026-08-04 09:43:47 | 173 | ||||||
|
CalR Resource Report Resource Website 100+ mentions |
CalR (RRID:SCR_015849) | data processing software, data analysis software, software resource, software application, web application, data visualization software | A Web-based Analysis Tool for Indirect Calorimetry Experiments which measure physiological energy balance. It is a web application for indirect calorimetry analysis which generates customizable time, bar and regression plots for calorimetry data using two-, three-, and four-group templates. | indirect, calorimerty, analysis, visualization, energy, balance, food intake, energy expenditure, metabolism, metabolic phenotyping, CLAMS, PhenoMaster, Prometheon, biostatistics, ANCOVA, reproducibility, Columbus Instruments, Sable Systems, TSE | is related to: Harvard University; Cambridge; United States | Mouse Metabolic Phenotyping Center ; Harvard Digestive Disease Center ; NIDDK |
DOI:10.1101/213967 | Freely available, Public | https://calrapp.org | SCR_015849 | A Web Application for Indirect Calorimetry Analysis | 2026-08-04 09:43:45 | 196 | ||||||
|
BIAevaluation Software Resource Report Resource Website 100+ mentions |
BIAevaluation Software (RRID:SCR_015936) | data processing software, data analysis software, standalone software, software resource, software application, data visualization software | Analysis software for life science data. This software package is for presentation and evaluation of sensorgram data from real-time BIA analyses. | evaluation, life, science, bia, biacore, sensorgram, bia, analysis, real-time | Commercially Available, Available for purchase, License available for purchase | http://www.molecular-interactions.si/data/equipment/BIAeval3-AC.pdf | SCR_015936 | BIAevaluation Software Kit, BIAevaluation | 2026-08-04 09:43:46 | 457 | |||||||||
|
Pattern Component Modelling Toolbox Resource Report Resource Website 1+ mentions |
Pattern Component Modelling Toolbox (RRID:SCR_015891) | PCM | data processing software, software application, software resource, data analysis software | Software for a Bayesian approach for evaluating representational models that specify how complex patterns of neural activity relate to visual stimuli, motor actions, or abstract thoughts. PCM evaluates the ability of models to predict novel brain activity patterns and integrates over all possible activity profiles and computes the marginal likelihood of the data under the activity profile distribution specified by the representational model. | bayesian, representational, model, motor, abstract, visual, encoding, neural, imaging, activity, pattern, analysis, voxel | James McDonnell Foundation ; NSERC RGPIN-2016-04890; JSPS 15J03233 |
PMID:28843540 | Free, Available for download | SCR_015891 | Pattern component modeling (PCM), PCM Toolbox, Pattern Component Modeling toolbox for multivariate analysis | 2026-08-04 09:43:46 | 2 | |||||||
|
Gannet Resource Report Resource Website 100+ mentions |
Gannet (RRID:SCR_016049) | data processing software, source code, data analysis software, software resource, software application | Free, open-source MATLAB-based software toolkit for analyzing edited 1H magnetic resonance spectroscopy (MRS) data. | mri, magnetic resonance spectroscopy, mrs, batch, analysis, matlab, neuroscience, brain | PMID:25548816 | https://www.nitrc.org/projects/gannet/, https://markmikkelsen.github.io/Gannet-docs/index.html | http://www.gabamrs.com/about | SCR_016049 | Gannet - Batch Analysis of Edited Magnetic Resonance Spectroscopy (MRS) Data | 2026-08-04 09:43:48 | 149 | ||||||||
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HiLive Resource Report Resource Website |
HiLive (RRID:SCR_016134) | data processing software, data analysis software, software resource, sequence analysis software, software application | Software tool for performing read mapping that maps Illumina HiSeq sequencer read alignments when they are produced. Used in Next Generation Sequencing in time critical, clinical applications. | perform, read, mapping, sequence, alignment, analysis, Illumina, time, critical, clinical, application |
is listed by: Debian is listed by: OMICtools |
the German Federal Ministry of Health IIA5-2512-FSB-725 | PMID:27794555 | Free, Available for download | OMICS_13393 | https://sources.debian.org/src/hilive/ | https://sourceforge.net/projects/hilive/ | SCR_016134 | 2026-08-04 09:43:49 | 0 | |||||
|
jamovi Resource Report Resource Website 1000+ mentions |
jamovi (RRID:SCR_016142) | data processing software, software application, software resource, data analysis software | Software for statistical analysis and spreadsheet editing that is built on top of the R statistical language. It encourages a “community driven” philosophy, where users can develop and publish their analyses to make them available to a wide audience. | spreadsheet, r, statistic, methodology, r, package, analysis | Free, Available for download | SCR_016142 | the jamovi project | 2026-08-04 09:43:49 | 2851 | ||||||||||
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GARLI Resource Report Resource Website 100+ mentions |
GARLI (RRID:SCR_016117) | GARLI | data processing software, software application, software resource, data analysis software | Software application for inferring phylogenetic trees and analysis of molecular sequence data using the maximum-likelihood criterion. It implements nucleotide, amino acid and codon-based models of sequence evolution. | inference, phylogenetic, tree, analysis, molecular, sequence, data, maximum, likelihood, criterion, nucleotide, amino acid, codon, model, evolution |
is listed by: Debian is listed by: OMICtools |
Free, Available for download, Freely available | OMICS_04234 | https://code.google.com/archive/p/garli/, https://sources.debian.org/src/garli/ | SCR_016117 | Genetic Algorithm for Rapid Likelihood Inference | 2026-08-04 09:43:49 | 279 | ||||||
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Fsm-lite Resource Report Resource Website 10+ mentions |
Fsm-lite (RRID:SCR_016115) | data processing software, software application, software resource, data analysis software | Software application as a single-core implementation of frequency-based substring mining. It can be used in bioinformatics to extract substrings that discriminate two (or more) datasets inside high-throughput sequencing data. | protein, dna, rna, sequence, analysis, core, implementation, frequency, based, substring, mining, extract, discriminate, dataset, sequencing, high throughput |
is listed by: Debian is listed by: OMICtools |
Free, Available for download | OMICS_28406 | https://sources.debian.org/src/fsm-lite/ | SCR_016115 | fsm, Frequency-based String Mining, Frequency-based String Mining (lite) | 2026-08-04 09:43:49 | 15 | |||||||
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DIAMOND Resource Report Resource Website 100+ mentions |
DIAMOND (RRID:SCR_016071) | data processing software, data analysis software, software resource, sequence analysis software, software application | Software that performs sequence alignment for protein and translated DNA searches and functions. Used for high performance analysis of big sequence data, protein-protein search, and DNA-protein search. | sequence, aligner, high, performance, analysis, big, data, protein, DNA, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools has parent organization: University of Tubingen; Tubingen; Germany |
PMID:25402007 DOI:10.1038/nmeth.3176 |
Free, Available for download | OMICS_08011, biotools:diamond | https://bio.tools/diamond, https://sources.debian.org/src/diamond-aligner/ | SCR_016071 | 2026-08-04 09:43:48 | 386 |
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