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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SimPhy Resource Report Resource Website 1+ mentions |
SimPhy (RRID:SCR_024501) | simulation software, software application, software resource | Software package for simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer, all three potentially leading to species tree/gene tree discordance and gene conversion. Used for phylogenomic simulation of gene, locus, and species trees. | phylogenomic simulation, gene phylogenomic simulation, locus phylogenomic simulation, species trees phylogenomic simulation, | is listed by: SoftCite | PMID:26526427 | Free, Available for download, Freely available | SCR_024501 | 2026-09-12 01:00:48 | 1 | |||||||||
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Mutation Assessor Resource Report Resource Website 500+ mentions |
Mutation Assessor (RRID:SCR_024502) | software resource, web application | Web server predicts functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or missense polymorphisms. Functional impact is assessed based on evolutionary conservation of affected amino acid in protein homologs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | functional impact of amino-acid substitutions in proteins prediction, | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_024502 | 2026-09-12 01:00:48 | 535 | ||||||||||
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CRISPResso2 Resource Report Resource Website 50+ mentions |
CRISPResso2 (RRID:SCR_024503) | data analysis software, data processing software, software application, software resource | Software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments. Used for analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments. | sequencing data analysis, genome editing experiments interpretation, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024503 | 2026-09-12 01:00:48 | 61 | ||||||||||
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OpenBUGS Resource Report Resource Website 100+ mentions |
OpenBUGS (RRID:SCR_024488) | data analysis software, data processing software, software application, software resource | Software for analysing complex statistical models using Markov chain Monte Carlo methods. | analysing complex statistical models, Markov chain Monte Carlo method, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024488 | Open Bayesian inference Using Gibbs Sampling | 2026-09-12 01:00:48 | 161 | |||||||||
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AutoRT Resource Report Resource Website 1+ mentions |
AutoRT (RRID:SCR_024513) | simulation software, software application, software resource | Software tool for peptide retention time prediction using deep learning. Supports peptide retention prediction for tryptic peptides, MHC bound peptides and PTM peptides. | proteogenomics analysis | is listed by: SoftCite | PMID:32273506 | Free, Available for download, Freely available | SCR_024513 | 2026-09-12 01:00:48 | 3 | |||||||||
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ModFOLD Resource Report Resource Website 1+ mentions |
ModFOLD (RRID:SCR_024518) | data access protocol, software resource, web service | Web server for the global and local quality estimation of 3D protein models | quality estimation, 3D protein models, | is listed by: SoftCite | PMID:28460136 | Restricted | SCR_024518 | ModFOLD6, ModFOLD8 | 2026-09-12 01:00:48 | 5 | ||||||||
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Metscape Resource Report Resource Website 100+ mentions |
Metscape (RRID:SCR_014687) | resource, software resource, source code | A software program that allows users to visualize and interpret human metabolim and expression profiling data by providing users with a bioinformatics framework. Its features include bulding and analyzing networks of genes and compounds, identifying enriched pathways from expression profiling data, and visualizing changes in metabolite data. | metabolomics, metabolomics tool, visualization, expression profiling, gene, compound, metabolism, human |
is listed by: Metabolomics Workbench is listed by: SoftCite |
NIDDK U24 DK097153; NIDDK P30DK089503 |
PMID:22135418 | Freely available | SCR_014687 | 2026-09-12 01:00:51 | 154 | ||||||||
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MINC Resource Report Resource Website 100+ mentions |
MINC (RRID:SCR_002391) | MINC | data processing software, image analysis software, software application, software resource | A medical imaging data format and an associated set of tools and libraries including a 3 level API for medical image analysis with a particular focus on the needs of research. There are also a number of tools including Registration and Non-Uniformity correction. | reusable library, c, file format, fortran, information specification, minc, minc2, magnetic resonance, os independent, perl, sh/bash, unix shell |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: SoftCite is related to: MINC Example files is related to: Extensible MATLAB Medical image Analysis has parent organization: McConnell Brain Imaging Center |
Free, Available for download, Freely available | nlx_155794 | http://www.nitrc.org/projects/minc | SCR_002391 | MINC - Medical Image NetCDF, Medical Imaging NetCDF | 2026-09-12 01:00:53 | 126 | ||||||
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OpenEpi Resource Report Resource Website 100+ mentions |
OpenEpi (RRID:SCR_021913) | data analytics software, software application, software resource, software toolkit | Web based, open source, operating system independent series of programs designed for use in public health and medicine for training or practice that provide number of epidemiologic and statistical tools for summary data. Developed in JavaScript and HTML, and can be run in modern web browsers. Program can be run from OpenEpi website or downloaded and run without web connection. | epidemiologic tool, statistical tool, epidemiologic statistics, public health |
is listed by: SoftCite has parent organization: Emory University; Georgia; USA |
Bill and Melinda Gates Foundation | PMID:19445426 | Free, Available for download, Freely available | SCR_021913 | 2026-09-12 01:00:22 | 160 | ||||||||
|
REDCap Resource Report Resource Website 10000+ mentions |
REDCap (RRID:SCR_003445) | REDCap | software resource, web application | Web application that allows users to build and manage online surveys and databases. Using REDCap's stream-lined process for rapidly developing projects, you may create and design projects using 1) the online method from your web browser using the Online Designer; and/or 2) the offline method by constructing a "data dictionary" template file in Microsoft Excel, which can be later uploaded into REDCap. Both surveys and databases (or a mixture of the two) can be built using these methods. REDCap provides audit trails for tracking data manipulation and user activity, as well as automated export procedures for seamless data downloads to Excel, PDF, and common statistical packages (SPSS, SAS, Stata, R). Also included are a built-in project calendar, a scheduling module, ad hoc reporting tools, and advanced features, such as branching logic, file uploading, and calculated fields. REDCap has a quick and easy software installation process, so that you can get REDCap running and fully functional in a matter of minutes. Several language translations have already been compiled for REDCap (e.g. Chinese, French, German, Portuguese), and it is anticipated that other languages will be available in full versions of REDCap soon. The REDCap Shared Library is a repository for REDCap data collection instruments and forms that can be downloaded and used by researchers at REDCap partner institutions. | online survey, survey, database, translational research, informatics, workflow, clinical research, clinical, metadata, biomedical, online form, data capture, management, analysis, data sharing, data collection, data standard, best practice, data collection instrument, electronic data capture |
is listed by: Biositemaps is listed by: SoftCite is related to: Clinical and Translational Science Awards Consortium has parent organization: Vanderbilt University; Tennessee; USA works with: redcap-completion works with: aux-file-upload |
NIH ; UL1 RR029882 ; UL1 TR000062 ; UL1 RR026314 ; UL1 TR000077 ; UL1 RR024975 ; UL1 TR000445 ; G12 RR003051 ; G12 MD007600 ; UL1 RR024150 ; UL1 TR000135 ; R24 HD042849 ; UL1 RR024989 ; UL1 TR000439 |
PMID:23149159 PMID:18929686 |
Software is available at no cost for REDCap Consortium Partners. If not in the consortium, See the Become a Partner page to find more information about joining our group. | nif-0000-33254 | SCR_003445 | RED Cap, Research Electronic Data Capture, The REDCap Consortium | 2026-09-12 01:00:35 | 23733 | |||||
|
Vmatch Resource Report Resource Website 50+ mentions |
Vmatch (RRID:SCR_018968) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for efficiently solving large scale sequence matching tasks. | Sequence analysis, large scale, sequence matching, sequence, matching, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite has parent organization: University of Hamburg; Hamburg; Germany |
Free, Available for download, Freely available | OMICS_19963, biotools:vmatch | https://bio.tools/vmatch, https://sources.debian.org/src/vmatch/ | SCR_018968 | 2026-09-12 12:59:08 | 56 | ||||||||
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Leica QWin Resource Report Resource Website 1+ mentions |
Leica QWin (RRID:SCR_018940) | data processing software, image analysis software, image processing software, software application, software resource | Software tool as image analysis and processing solution for quantitative microscopy which provides control of Leica microscopes and Leica digital cameras. Capability ranges from simple interactive image measurements to automatic, multi-parameter measurements. Available in editions including QWin Runner, QWin Lite, QWin Plus, QWin Standard and QWin Professional. | Leica, microscope, digital camera, image analysis, image processing, quantitative microscopy | is listed by: SoftCite | Restricted | http://www.mcbainsystems.com/pdf/Leica_QWin.pdf | SCR_018940 | 2026-09-12 12:59:08 | 5 | |||||||||
|
PAST Resource Report Resource Website 100+ mentions |
PAST (RRID:SCR_019129) | data analysis software, data processing software, software application, software resource | Software package for education and data analysis. Used for scientific data analysis, with functions for data manipulation, plotting, univariate and multivariate statistics, ecological analysis, time series and spatial analysis, morphometrics and stratigraphy. | Paleontological statistics, data analysis, data manipulation function, data plotting, multivariate statistics, ecological analysis, spatial analysis, morphometrics, stratography | is listed by: SoftCite | Free, Available for download, Freely available | SCR_019129 | PAST 4.03, PAleontological STatistics | 2026-09-12 12:59:10 | 153 | |||||||||
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MSQuant Resource Report Resource Website 1+ mentions |
MSQuant (RRID:SCR_019206) | data analysis software, data analytics software, data processing software, software application, software resource | Software tool for quantitative proteomics,mass spectrometry and processes spectra and LC runs to find quantitative information about proteins and peptides. Though automated it also allows manual inspection and change.Entry in MSQuant is Mascot search engine. | Qantitative proteomics, mass spectrometry, spectra processes, LC runs, protein, peptide |
uses: Mascot is listed by: SoftCite |
Free, Available for download | http://msquant.alwaysdata.net/ | SCR_019206 | 2026-09-12 12:59:10 | 4 | |||||||||
|
biomaRt Resource Report Resource Website 1000+ mentions |
biomaRt (RRID:SCR_019214) | data analysis software, data processing software, software application, software resource | Software package that integrates BioMart data resources with data analysis software in Bioconductor. Can annotate range of gene or gene product identifiers including Entrez Gene and Affymetrix probe identifiers with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis. | BioMart databases, Bioconductor, data analysis, BioMart data integration, gene annotation, gene product identifiers annotation, gene symbol retrival, chromosomal coordinates retrival, genomic sequence retrival, nucleotide polimorphism information, , bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: BioMart Project is related to: BioMart MartView is related to: Entrez Gene is related to: Affymetrix is related to: Gene Ontology is related to: OMIM is related to: Affymetrix |
PMID:16082012 | Free, Available for download, Freely available | biotools:biomart | https://bio.tools/biomart | SCR_019214 | biomaRt v 2.42.1 | 2026-09-12 12:59:10 | 2879 | ||||||
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PAUP Resource Report Resource Website 1000+ mentions |
PAUP (RRID:SCR_014931) | PAUP | data analysis software, data processing software, data visualization software, software application, software resource | Software which creates phylogenetic trees from molecular, morphological and/or behavioral data through high speed computer analysis. | phylogenetic tree, phylogeny, evolutionary tree, molecular data, morphological data, behavioral data |
is listed by: SoftCite works with: PAML |
Free | http://people.sc.fsu.edu/~dswofford/paup_test/ | SCR_014931 | Phylogenetic Analysis Using Parsimony | 2026-09-12 12:58:23 | 2292 | |||||||
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Nexus Resource Report Resource Website 100+ mentions |
Nexus (RRID:SCR_015001) | data acquisition software, data processing software, software application, software resource | Data capture software for use with Vicon motion capture system. Its features include MATLAB integration, Python pre-installed, customized workflow, and automated quality assessment. | biomechanics, motion capture |
is listed by: SoftCite works with: MATLAB works with: Bodybuilder |
Available for download | https://www.vicon.com/downloads/core-software/nexus | SCR_015001 | Nexus 2, Nexus 1.8.5, Nexus 2.5.0, Nexus 2.4.0 | 2026-09-12 12:58:24 | 397 | ||||||||
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Statgraphics Centurion Resource Report Resource Website 1+ mentions |
Statgraphics Centurion (RRID:SCR_015248) | data analysis software, data processing software, data visualization software, software application, software resource | Data analysis and visualization software with features that include a R interface, demographic maps, bivariate density estimation, multiple time series visualization, repeated ANOVA measures, and a multivariate visualizers. | statistical analysis software, statistical visualization software, statistical analysis | is listed by: SoftCite | Available for download, Trial available, Available for purchase | SCR_015248 | Statgraphics Centurion XVII | 2026-09-12 12:58:26 | 7 | |||||||||
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MPlus Resource Report Resource Website 1000+ mentions |
MPlus (RRID:SCR_015578) | data analysis software, data processing software, simulation software, software application, software resource | Statistical modeling program that provides a wide choice of models, estimators, and algorithms in a program that has graphical displays of data and analysis results. Mplus allows the analysis of both cross-sectional and longitudinal data, single-level and multilevel data, data that come from different populations with either observed or unobserved heterogeneity, and data that contain missing values. Analyses can be carried out for observed variables that are continuous, censored, binary, ordered categorical (ordinal), unordered categorical (nominal), counts, or combinations of these variable types. In addition, Mplus has extensive capabilities for Monte Carlo simulation studies, where data can be generated and analyzed according to any of the models included in the program. The Mplus modeling framework draws on the unifying theme of latent variables. The generality of the Mplus modeling framework comes from the unique use of both continuous and categorical latent variables. Continuous latent variables are used to represent factors corresponding to unobserved constructs, random effects corresponding to individual differences in development, random effects corresponding to variation in coefficients across groups in hierarchical data, frailties corresponding to unobserved heterogeneity in survival time, liabilities corresponding to genetic susceptibility to disease, and latent response variable values corresponding to missing data. Categorical latent variables are used to represent latent classes corresponding to homogeneous groups of individuals, latent trajectory classes corresponding to types of development in unobserved populations, mixture components corresponding to finite mixtures of unobserved populations, and latent response variable categories corresponding to missing data. | statistical modeling software, data imaging software, software model, modeling estimator, modeling algorithms | is listed by: SoftCite | Available for purchase, Free demo available, Student pricing is available | SCR_015578 | Mplus Version 8 | 2026-09-12 12:58:28 | 1032 | |||||||||
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MetaboAnalyst Resource Report Resource Website 10000+ mentions |
MetaboAnalyst (RRID:SCR_015539) | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | 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 ; Canada Research Chairs Program ; Canadian Institutes for Health Research ; Genome Alberta ; Genome Canada ; McGill University ; Natural Sciences and Engineering Research Council of Canada |
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 | 2026-09-12 12:58:27 | 13689 |
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