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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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The Decoding Toolbox Resource Report Resource Website 10+ mentions |
The Decoding Toolbox (RRID:SCR_017424) | TDT | software application, data processing software, data analysis software, software resource | Software Matlab toolbox for multivariate analysis of functional and structural MRI data. Software package for multivariate analyses of functional imaging data. | Multivariate, analysis, structural, MRI, data, functional, imaging, brain | German Ministry of Education and Research ; German Research Foundation |
PMID:25610393 | Free, Available for download, Freely available | SCR_017424 | 2026-02-15 09:22:02 | 13 | ||||||||
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QtiPlot Resource Report Resource Website 10+ mentions |
QtiPlot (RRID:SCR_017311) | software application, data processing software, data analysis software, software resource | Software tool for data analysis and scientific visualization by IONDEV SRL. | data, analysis, visualization, IONDEV SRL | Restricted | SCR_017311 | 2026-02-15 09:22:02 | 28 | |||||||||||
|
vbSPT Resource Report Resource Website 1+ mentions |
vbSPT (RRID:SCR_017554) | software application, data processing software, data analysis software, software resource | Software package for analysis of single particle diffusion trajectories, where diffusion constants switch randomly according to Markov process. Analytical tool to combine information from thousands of short single-molecule trajectories of intracellularly diffusing proteins. Has ability to learn number of diffusive states directly from data, in addition to model parameters such as transition rates and diffusion constants. | Analysis, single, particle, diffusion, trajectory, Markov, short, molecule, intracellularly, protein, data, transition, state | PMID:23396281 | Free, Available for download, Freely available | https://sourceforge.net/projects/vbspt/files/latest/download?source=files | SCR_017554 | variational Bayes single particle tracking | 2026-02-15 09:22:08 | 3 | ||||||||
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Rotor-Gene 6000 series software Resource Report Resource Website 1+ mentions |
Rotor-Gene 6000 series software (RRID:SCR_017552) | software application, data processing software, data analysis software, software resource | Rotor-Gene real-time analysis software system for ROTOR GENE 6000 REAL-TIME PCR machine. Software has been refined to provide an intuitive, Wizard driven interface, enabling flexibility and automation. Build-in extensive analysis, graphing and statistical functions. Unlimited use software license for Windows XP, Pentium IV (2GHz) or higher PC. | Rotor, Gene, 6000 Real Time, PCR machine, analysis, graphing, statistical, function | Free, Available for download, Freely available | https://www.baylor.edu/content/services/document.php/187886.pd | SCR_017552 | Rotor-Gene 6000 series software 1.7 | 2026-02-15 09:22:03 | 3 | |||||||||
|
LabChart Reader Resource Report Resource Website 100+ mentions |
LabChart Reader (RRID:SCR_017551) | software application, data processing software, data analysis software, software resource | LabChart data analysis software creates a platform for all of your recording devices to work together, allowing you to acquire biological signals from multiple sources simultaneously and apply advanced calculations and plots as your experiment unfolds. LabChart Reader is free version of software that allows to analyse with some limitations. LabChart Reader doesn’t allow saving of data - export image only. Has data pad for analysis. | Adinstruments, LabChart, data, analysis, calculation, plot | is related to: LabChart | https://www.adinstruments.com/products/labchart/versions-and-licenses | SCR_017551 | LabChart Reader software 8.1, LabChart Reader software | 2026-02-15 09:22:05 | 141 | |||||||||
|
Mesquite Resource Report Resource Website 100+ mentions |
Mesquite (RRID:SCR_017994) | software application, data processing software, data analysis software, software resource | Software tool as modular system for evolutionary analysis. Software for evolutionary biology, designed to organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Analyses available depend on modules installed. Comes with many packages already installed. | Modular, evolutionary, analysis, organize, comparative data, organism, phylogenetic, population genetic, non-pylogenetic | is listed by: Debian | NSF DEB 1258220; David and Lucile Packard Foundation ; NSERC Discovery grant ; NSF |
Free, Available for download, Freely available | https://sources.debian.org/src/mesquite/ | SCR_017994 | Mesquite 3.04, Mesquite 3.61 | 2026-02-15 09:22:09 | 151 | |||||||
|
GENEPOP Resource Report Resource Website 1000+ mentions |
GENEPOP (RRID:SCR_009194) | Genepop | software application, data processing software, data analysis software, software resource | Population genetic data analysis software package. Used to perform exact Hardy Weinberg Equilibrium test. Used for population differentiation and for genotypic disequilibrium among pairs of loci. Computes estimates of F-statistics, null allele frequencies, allele size-based statistics for microsatellites, etc. and performs analyses of isolation by distance from pairwise comparisons of individuals or population samples., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Population, differentation, genetic, data, analysis, Hardy Weinberg Equilibrium test, statistics, genotyping, disequilibrium, pair, loci, allele, frequency |
is listed by: Genetic Analysis Software is listed by: CRAN |
PMID:21585727 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154337 | https://kimura.univ-montp2.fr/~rousset/Genepop.htm https://cran.r-project.org/web/packages/genepop/index.html |
SCR_009194 | genepop'007 | 2026-02-15 09:19:39 | 2266 | |||||
|
MACS Resource Report Resource Website 1000+ mentions |
MACS (RRID:SCR_013291) | MACS | software application, data processing software, data analysis software, software resource | Software Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity. | identify, transcript, factor, binding, site, model, based, analysis, CHIP Seq, short, read, sequencer, protein, DNA, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Dana-Farber Cancer Institute |
NHGRI HG004069; NHGRI HG004270; NIDDK DK074967 |
PMID:18798982 DOI:10.1186/gb-2008-9-9-r137 |
Free, Available for download, Freely available | OMICS_00446, biotools:macs | https://bio.tools/macs https://sources.debian.org/src/macs/ |
SCR_013291 | MACS - Model-based Analysis for ChIP-Seq, Model-based Analysis for ChIP-Seq, MACS2 | 2026-02-15 09:20:42 | 1325 | ||||
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Electrographic Seizure Analyzer Resource Report Resource Website 1+ mentions |
Electrographic Seizure Analyzer (RRID:SCR_016344) | software application, data processing software, data analysis software, software resource | Software to automate analysis of electrographic seizures based on EEG or LFP data, featuring customizable thresholds and parameters for event detection and parameter setting. | automate, analysis, electrographic, seizure, EEG, LFP, data, event, detection, parameter, setting | is related to: MATLAB | Free, Available for download, Freely available | SCR_016344 | 2026-02-15 09:21:38 | 5 | ||||||||||
|
BioJupies Resource Report Resource Website 50+ mentions |
BioJupies (RRID:SCR_016346) | web application, software resource | Software as an open source web server that automatically generates RNA-seq data analysis of jupyter notebooks. It allows creation and containment of documents that have live code, visualizations and narrative text. | automatically, generate, RNAseq, data, analysis, notebook, create, visualize, report, custom, raw, processed, user, interface | is affiliated with: Icahn School of Medicine at Mount Sinai; New York; USA | Free, Available for download, Freely available | SCR_016346 | 2026-02-15 09:21:51 | 65 | ||||||||||
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TRANSIT Resource Report Resource Website 1+ mentions |
TRANSIT (RRID:SCR_016492) | software application, data processing software, data analysis software, software resource | Software tool Python based and open source for statistical analysis of TnSeq data. Provides a graphical interface to three different statistical methods for analyzing TnSeq data capable of identifying essential genes in individual datasets as well as comparative analysis between conditions. | statistical, analysis, TnSeq, data, identify, gene, dataset, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Texas A and M University; Texas; USA |
PMID:26447887 | Free, Available for download, Freely available | biotools:transit | https://github.com/mad-lab/transit https://bio.tools/transit |
SCR_016492 | 2026-02-15 09:21:07 | 4 | |||||||
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rsfMRI_fconn calculation Resource Report Resource Website 1+ mentions |
rsfMRI_fconn calculation (RRID:SCR_016591) | rsfMRI_fconn calculation | software application, data processing software, data analysis software, 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 | 2026-02-15 09:21:53 | 1 | |||||||||
|
Motion Sensing Superpixels (MOSES) Resource Report Resource Website 1+ mentions |
Motion Sensing Superpixels (MOSES) (RRID:SCR_016839) | MOSES | software application, data processing software, data analysis software, 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 | 2026-02-15 09:21:55 | 1 | ||||||||
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Neurolucida 360 Resource Report Resource Website 10+ mentions |
Neurolucida 360 (RRID:SCR_016788) | software application, data processing software, data analysis software, software resource | Software for automatic neuron 3D reconstruction and analysis. Used by neuroscientists to reconstruct intricate neuronal structures that range in scale from complex, multicellular networks of neurons to sub-cellular dendritic spines and putative synapses. | mbf Bioscience, automatic, image, 3D, reconstruction, analysis, neuron, synapse, data | is used by: SPARC Portal | Commercially available, Free trial available | SCR_016788 | 2026-02-15 09:21:49 | 45 | ||||||||||
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Ragu Resource Report Resource Website 1+ mentions |
Ragu (RRID:SCR_016851) | Ragu | software application, data processing software, data analysis software, software resource | Software tool for the analysis of EEG and MEG event-related scalp field data using global randomization statistics. | statistical, analysis, EEG, MEG, electromagnetic, data, scalp, field | DOI:doi/10.1155/2011/938925 | SCR_016851 | Randomization Graphical User interface, Randomization Graphical User | 2026-02-15 09:21:50 | 3 | |||||||||
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riboSeqR Resource Report Resource Website 1+ mentions |
riboSeqR (RRID:SCR_016947) | software application, data processing software, data analysis software, 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 | 2026-02-15 09:21:56 | 4 | ||||||||||
|
scran Resource Report Resource Website 50+ mentions |
scran (RRID:SCR_016944) | SCRAN | software application, data processing software, data analysis software, 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 ; 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 | 2026-02-15 09:21:52 | 92 | ||||
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ConsensusClusterPlus Resource Report Resource Website 100+ mentions |
ConsensusClusterPlus (RRID:SCR_016954) | software application, data processing software, data analysis software, 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; Thomas G. Labrecque Foundation ; NCI U24 CA126554 |
PMID:20427518 | Free, Available for download, Freely available | biotools:consensusclusterplus | https://bio.tools/consensusclusterplus | SCR_016954 | 2026-02-15 09:21:56 | 160 | ||||||
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mixOmics Resource Report Resource Website 50+ mentions |
mixOmics (RRID:SCR_016889) | software application, data processing software, data analysis software, 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 | 2026-02-15 09:21:50 | 58 | ||||||||||
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Wizard Resource Report Resource Website 1+ mentions |
Wizard (RRID:SCR_016939) | software application, data processing software, data analysis software, software resource | Software tool for data analysis and exploration. Statistics software for Mac. | statistics, software, Mac, data, analysis | Commercially available, Free trial available, Tutorial available | https://www.macupdate.com/app/mac/50415/wizard | SCR_016939 | Wizard 1.9.28, Wizard 1.9.27, Wizardmac | 2026-02-15 09:21:52 | 4 |
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