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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BIAevaluation Software Resource Report Resource Website 100+ mentions |
BIAevaluation Software (RRID:SCR_015936) | data analysis software, data processing software, data visualization software, software application, software resource, standalone 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 | 2026-09-05 06:28:01 | 459 | |||||||||
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Pattern Component Modelling Toolbox Resource Report Resource Website 1+ mentions |
Pattern Component Modelling Toolbox (RRID:SCR_015891) | PCM | data analysis software, data processing software, software application, software resource | 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 ; JSPS 15J03233; NSERC RGPIN-2016-04890 |
PMID:28843540 | Free, Available for download | SCR_015891 | Pattern component modeling (PCM), PCM Toolbox, Pattern Component Modeling toolbox for multivariate analysis | 2026-09-05 06:28:00 | 3 | |||||||
|
Ariba Resource Report Resource Website 100+ mentions |
Ariba (RRID:SCR_015976) | data analysis software, data processing software, sequence analysis software, software application, software resource, 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 |
Biotechnology and Biological Sciences Research Council BB/M014088/1; Wellcome Trust 206194 |
PMID:29177089 DOI:10.1099/mgen.0.000131 |
Free, Available for download, Freely available | OMICS_17327 | https://sources.debian.org/src/artemis/ | SCR_015976 | 2026-09-05 06:28:01 | 220 | ||||||
|
Autogrid Resource Report Resource Website 1000+ mentions |
Autogrid (RRID:SCR_015982) | data analysis software, data processing software, simulation software, software application, software resource | 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 | 2026-09-05 06:28:01 | 1261 | ||||||
|
Atac Resource Report Resource Website 1000+ mentions |
Atac (RRID:SCR_015980) | alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource | 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 | 2026-09-05 06:28:01 | 1826 | |||||||
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Axe Resource Report Resource Website 1+ mentions |
Axe (RRID:SCR_015984) | data analysis software, data processing software, sequence analysis software, software application, software resource, 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 | 2026-09-05 06:28:02 | 1 | |||||||
|
Bamtools Resource Report Resource Website 100+ mentions |
Bamtools (RRID:SCR_015987) | data analysis software, data management software, data processing software, software application, software resource, 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 | 2026-09-05 06:28:02 | 344 | ||||||
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Gannet Resource Report Resource Website 100+ mentions |
Gannet (RRID:SCR_016049) | data analysis software, data processing software, software application, software resource, source code | 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 | 2026-09-05 06:28:02 | 167 | ||||||||
|
MRTool Resource Report Resource Website 10+ mentions |
MRTool (RRID:SCR_015956) | data or information resource, portal, topical portal | 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 | 2026-09-05 06:28:01 | 14 | |||||||||
|
scater Resource Report Resource Website 100+ mentions |
scater (RRID:SCR_015954) | data analysis software, data processing software, data visualization software, sequence analysis software, software application, software resource, 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 |
Cancer Research UK A17197; European Molecular Biology Laboratory ; National Health and Medical Research Council of Australia APP1112681; Oxford Single Cell Biology Consortium ; United Kingdom Medical Research Council |
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) | 2026-09-05 06:28:01 | 187 | ||||||
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DIAMOND Resource Report Resource Website 100+ mentions |
DIAMOND (RRID:SCR_016071) | data analysis software, data processing software, sequence analysis software, software application, software resource | 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 | 2026-09-05 06:28:03 | 489 | |||||||
|
loadGtfToGe_db Resource Report Resource Website 1+ mentions |
loadGtfToGe_db (RRID:SCR_015998) | data processing software, data visualization software, software application, software resource | One stop platform for NGS big data from analysis to visualization. There are about 400 analysis pipelines integrated on Maser. List of all analysis pipelines, including descriptions and approximate execution times, can be found on page for ‘All pipelines’ in the User Guide. loadGtfToGe_db software loads GTF files to a database for Genome Explorer. It allows the user to browse the results through the GE. | analysis, pipeline, maser, genome, explorer, upload, database, browse | Ministry of Education ; Culture ; Sports ; Science and Technology ; Japan |
Restricted | http://cell-innovation.nig.ac.jp/maser_cgi/cip-pl_list_violin_en.cgi | SCR_015998 | Management and Analysis System for Enormous Reads: loadGtfToGe_db | 2026-09-05 06:28:02 | 1 | ||||||||
|
Datamash Resource Report Resource Website 1+ mentions |
Datamash (RRID:SCR_016067) | data analysis software, data processing software, software application, software resource | Software for a command-line interface which performs basic numeric, textual and statistical operations on input textual data files. It is designed to aid researchers in automating analysis pipelines, without writing code or short scripts. | command-line, interface, basic, numerical, textual, statistical, operation, input, data, files, automate, analysis, pipelines | is listed by: Debian | Free Software Foundation (FSF) | Free, Available for download | https://sources.debian.org/src/datamash/ | SCR_016067 | GNU Datamash | 2026-09-05 06:28:03 | 4 | |||||||
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HiLive Resource Report Resource Website |
HiLive (RRID:SCR_016134) | data analysis software, data processing software, sequence analysis software, software application, software resource | 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 | 2026-09-05 06:28:04 | 0 | |||||
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jamovi Resource Report Resource Website 1000+ mentions |
jamovi (RRID:SCR_016142) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-05 06:28:04 | 4164 | ||||||||||
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SymPhoTime 64 Resource Report Resource Website 10+ mentions |
SymPhoTime 64 (RRID:SCR_016263) | data acquisition software, data processing software, data visualization software, image acquisition software, image analysis software, software application, software resource | Software for fluorescence lifetime imaging and correlation. SymPhoTime 64 is the data acquisition software for PicoQuant's time-resolved confocal microscope MicroTime 200 and LSM upgrade kits. | fluorescent, imaging, correlation, microscope, companion software, image, analysis, microscopy, image acquisition | Commercially available, Free, Available for download | SCR_016263 | SymPhoTime | 2026-09-05 06:28:06 | 13 | ||||||||||
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Raven Resource Report Resource Website 500+ mentions |
Raven (RRID:SCR_016190) | data analysis software, data processing software, data visualization software, software application, software resource | Software for the acquisition, visualization, measurement, and analysis of sounds. Raven supports annotations for research-related analysis. | audio, sound, analysis, acquisition, visualization, bird, avian, birdsong | has parent organization: Cornell University; New York; USA | Free, Available for download, Available for purchase, Commercially available, Tutorial available | https://store.birds.cornell.edu/ProductDetails.asp?ProductCode=RAVENLITE | SCR_016190 | 2026-09-05 06:28:05 | 869 | |||||||||
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FITMASTER Resource Report Resource Website 100+ mentions |
FITMASTER (RRID:SCR_016233) | data analysis software, data processing software, software application, software resource | Software for analysis and fitting routines of electrophysiological data. Analysis can be performed on the levels of Sweeps/Traces and Series. | electrophysiology, analysis, fitting, statistic, polynomial, exponential, gaussian, boltzmann, formalism, voltage, current | Free, Available for download, Tutorial available, Demo available | SCR_016233 | HEKA FITMASTER | 2026-09-05 06:28:05 | 101 | ||||||||||
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GARLI Resource Report Resource Website 100+ mentions |
GARLI (RRID:SCR_016117) | GARLI | data analysis software, data processing software, software application, software resource | 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 | 2026-09-05 06:28:04 | 280 | ||||||
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Fsm-lite Resource Report Resource Website 10+ mentions |
Fsm-lite (RRID:SCR_016115) | data analysis software, data processing software, software application, software resource | 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) | 2026-09-05 06:28:04 | 19 |
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