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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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JASP Resource Report Resource Website 1000+ mentions |
JASP (RRID:SCR_015823) | data analysis software, data processing software, software application, software resource | Statistics software that performs common frequentist analyses and Bayesian analyses. It conducts ANOVA, linear regression, and correlation, among other statistical tests. | statistical analysis, data analysis, statistical test, frequentist analysis, bayesian analysis, r package |
uses: R Project for Statistical Computing is listed by: SoftCite |
European Research Council | PMID:28685272 | Open source, Free, Available for download, Tutorial available, Runs on Windows, Runs on MAC OS, Runs on Linux | https://github.com/jasp-stats/jasp-desktop | SCR_015823 | 2026-09-03 04:53:12 | 4695 | |||||||
|
MCODE Resource Report Resource Website 1000+ mentions |
MCODE (RRID:SCR_015828) | algorithm resource, data analysis software, data processing software, image analysis software, software application, software resource | Software that clusters a given network based on topology to find densely connected regions. It can be used to find protein complexes and parts of pathways in protein-protein interaction networks or protein families in protein similarity networks. | cluster, clustering, graph analysis, network, network topology, interconnectivity | is listed by: SoftCite | Canadian Institutes of Health Research (CIHR) ; MDS-Sciex ; Ontario Research and Development Challenge Fund |
PMID:12525261 PMID:25570063 |
Free, Available for download | http://baderlab.org/Software/MCODE | SCR_015828 | 2026-09-03 04:53:24 | 1254 | |||||||
|
Poretools Resource Report Resource Website 50+ mentions |
Poretools (RRID:SCR_015879) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software toolkit for analyzing nanopore sequence data. | nanopore, sequence, python, oxford nanopore, MinION, quality control, downstream analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
Medical Research Council ; NHGRI R01 HG006693 |
PMID:25143291 | Open source, Free, Available for download | biotools:poretools | https://bio.tools/poretools | SCR_015879 | 2026-09-03 04:53:26 | 83 | ||||||
|
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 | 2026-09-03 04:53:29 | 1261 | ||||||
|
Ligprep Resource Report Resource Website 50+ mentions |
Ligprep (RRID:SCR_016746) | Ligprep | simulation software, software application, software resource | Software tool to correct and optimize the ligands by generating different protonation states, stereochemistry, tautomers, and ring conformations. Used to generate accurate, energy minimized 3D molecular structures. | correct, optimize, ligand, protonation, stereochemistry, tautomer, conformation, energy, minimized, 3D, moleular, structure |
is listed by: OMICtools is listed by: SoftCite has parent organization: Schrodinger works with: Glide works with: Phase |
Commercially available | SCR_016746 | LigPrep, LigandPreparation, Ligand preparation | 2026-09-03 04:54:01 | 50 | ||||||||
|
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 | 2026-09-03 04:59:06 | 23733 | |||||
|
V3D Resource Report Resource Website 1+ mentions |
V3D (RRID:SCR_008646) | V3D | d visualization software, data processing software, data visualization software, image analysis software, segmentation software, software application, software resource | V3D is a handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects. It also provides many unique functions, is Open Source, supports a very simple and powerful plugin interface and thus can be extended & enhanced easily. V3D-Neuron is a powerful 3D neuron reconstruction, visualization, and editing software built on top of V3D. Both V3D and V3D-Neuron have recently been published in Nature Biotechnology (April, 2010), and Highlighted in Nature Methods (May, 2010), and Science News (April, 2010), etc. V3D is a cross-platform (Mac, Linux, and Windows) tool for visualizing large-scale (gigabytes, and 64-bit data) 3D image stacks and various surface data. It is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management. This makes V3D suitable for various bioimage informatics applications, and a nice platform to develop new 3D image analysis algorithms for high-throughput processing. In short, V3D streamlines the workflow of visualization-assisted analysis. In the latest V3D development, it can render 5D (spatial-temporal) data directly in 3D volume-rendering mode; it supports convenient and interactive local and global 3D views at different scales. It even has a Matlab file IO toolbox. A user can now write his/her own plugins to take advantage of the V3D platform very easily. | 3d, annotation, bioimage, brain, cell, development, informatics, neuron, registration, segmentation, software, tracing, visual, visualization, image |
is listed by: SoftCite has parent organization: Janelia Research |
Howard Hughes Medical Institute | PMID:20231818 | nif-0000-32975 | SCR_008646 | V3D: A Swiss army knife for bioimage visualization & analysis | 2026-09-03 04:58:08 | 3 | ||||||
|
FASTA Resource Report Resource Website 500+ mentions |
FASTA (RRID:SCR_011819) | FASTA | data analysis software, data processing software, sequence analysis software, software application, software resource | Software package for DNA and protein sequence alignment to find regions of local or global similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence. | sequence, alignment, DNA, protein, similarity, searching |
is listed by: OMICtools is listed by: SoftCite has parent organization: European Bioinformatics Institute |
Free, Freely available | OMICS_00994 | SCR_011819 | Federal Acquisition STreamlining Act | 2026-09-03 04:58:16 | 896 | |||||||
|
DESeq2 Resource Report Resource Website 10000+ mentions |
DESeq2 (RRID:SCR_015687) | data analysis software, data processing software, software application, software resource, software tool | Software package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. | differential, gene, expression, analysis, binominal, distribution, RNA-seq data, Bioconductor, bio.tools |
is used by: Glimma is used by: TEtranscripts is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: SARTools works with: tximport |
European Union’s 7th Framework Programme ; International Max Planck Research School for Computational Biology and Scientific Computing ; NCI T32 CA009337 |
Free, Available for download, Freely available | biotools:deseq2 | https://github.com/mikelove/DESeq2, https://bio.tools/deseq2 | SCR_015687 | 2026-09-03 04:58:06 | 50789 | |||||||
|
Pipeline Pilot Resource Report Resource Website 100+ mentions |
Pipeline Pilot (RRID:SCR_014917) | data analysis software, data processing software, software application, software resource | Software used to automate the process of accessing, analyzing and reporting scientific data. This software can be used by a person with little or no software development experience can create scientific protocols that can be executed through a variety of interfaces including: BIOVIA Web Port, other BIOVIA solutions such as BIOVIA Electronic Lab Notebook, Isentris, Chemical Registration and third-party applications such as Microsoft SharePoint. The protocols aggregate and provide immediate access to volumes of research data, they automate the scientific analysis of data and allow researchers to explore, visualize and report results. | automation, accessing, analysis, analyzing, scientific data, aggregation. aggregate, research, scientific | is listed by: SoftCite | Commercial | SCR_014917 | 2026-09-03 04:58:23 | 358 | ||||||||||
|
RepeatModeler Resource Report Resource Website 1000+ mentions |
RepeatModeler (RRID:SCR_015027) | data analysis software, data processing software, sequence analysis software, software application, software resource | Sequence analysis software that performs repeat family identification and creates models for sequence data. RepeatModeler utilizes RepeatScout and RECON to identify repeat element boundaries and family relationships., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequence analysis, sequence repeats, repeat identification, bio.tools |
uses: RepeatScout is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Dfam |
Institute for Systems Biology ; NHGRI R44 HG02244; NHGRI R01 HG002939 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:repeatmodeler | https://bio.tools/repeatmodeler | SCR_015027 | 2026-09-03 04:58:24 | 3249 | |||||||
|
CMap Resource Report Resource Website 500+ mentions |
CMap (RRID:SCR_016204) | data or information resource, data set, database, software resource, web application | Dataset of cellular signatures that catalogs transcriptional responses of human cells to chemical and genetic perturbation. CMap contains perturbagens, expression signatures, and small molecules from cell lines. | data, set, connectivity, gene, expression, database, heat map, drug, tool, perturbational, perturbagen, signature, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Broad Institute |
Free for academic use, Subscription for commercial use, Available for download, Acknowledgement requested | biotools:CMap | https://bio.tools/CMap | SCR_016204 | LINCS CMap L1000, LINCS L1000, LINCS CMap, ConnectivityMap, Connectivity Map | 2026-09-03 04:58:23 | 789 | |||||||
|
pheatmap Resource Report Resource Website 1000+ mentions |
pheatmap (RRID:SCR_016418) | pheatmap | data acquisition software, data processing software, image acquisition software, software application, software resource, software toolkit | Software tool as a function in R to draw clustered heatmaps for better control over graphical parameters. | draw, clustered, heatmap, control, graphical, parameter, size, shape, text, bio.tools |
is used by: ClustVis is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite is related to: CRAN |
Free, Available for download, Freely available | biotools:pheatmap, OMICS_26726 | https://github.com/raivokolde/pheatmap, https://cran.r-project.org/web/packages/pheatmap/pheatmap.pdf, https://bio.tools/pheatmap, https://sources.debian.org/src/r-cran-pheatmap/ | SCR_016418 | pretty heatmap | 2026-09-03 04:58:26 | 1249 | ||||||
|
Protein preparation Wizard Resource Report Resource Website 10+ mentions |
Protein preparation Wizard (RRID:SCR_016749) | simulation software, software application, software resource | Software tool for correcting common structural problems and creating reliable, all atom protein models. | correcting, structural, problem, atom, protein, model, virtual, docking, method |
is listed by: SoftCite has parent organization: Schrodinger |
Commercially available, Training available | SCR_016749 | protein preparation wizard, Protein Preparation Wizard | 2026-09-03 04:58:25 | 13 | |||||||||
|
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 | 2026-09-03 04:58:39 | 160 | ||||||||
|
MediaWiki Resource Report Resource Website 10+ mentions |
MediaWiki (RRID:SCR_014045) | authoring tool, software application, software resource | A server-based software wiki package written in PHP. It is a powerful, scalable software deigned for high-traffic websites. MediaWiki uses PHP to process and display data stored in a database such as MySQL. When a user submits an edit to a page, MediaWiki writes it to the database without deleting the previous versions, allowing easy reversions. MediaWiki is able to manage image and multimedia files, as well, which are stored in the filesystem. | authoring tool, software, wiki, PHP, FASEB list |
is listed by: SoftCite is related to: WorkingWiki is parent organization of: Semantic MediaWiki |
Public, Free | SCR_014045 | 2026-09-03 04:52:33 | 49 | ||||||||||
|
HomeCageScan Resource Report Resource Website 10+ mentions |
HomeCageScan (RRID:SCR_014253) | data acquisition software, data analysis software, data processing software, software application, software resource, time-series analysis software | Software used for automatic high throughput analysis of unconstrained rodent behaviors in a home cage. HomeCageScan is ideal for longitudinal studies where several animals are studied and tested over long periods. Its features include twenty-four-hour recording capabilities, statistical analysis, automatic adaptation to environmental changes (including day and night changes), and a batch‐mode which allows user to run multiple videos successively without human intervention. The software can detect various behaviors ranging from feeding and urination to jumping and foraging. | automatic high throughput analysis, unconstrained rodent behavior, home cage, longitudinal study | is listed by: SoftCite | Available for purchase | SCR_014253 | 2026-09-03 04:52:39 | 30 | ||||||||||
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Adobe Photoshop Resource Report Resource Website 10000+ mentions |
Adobe Photoshop (RRID:SCR_014199) | data processing software, image analysis software, image processing software, software application, software resource | Software for image processing, analysis, and editing. The software includes features such as touch capabilities, a customizable toolbar, 2D and 3D image merging, and Cloud access and options. | image processing software, image analysis software, image editing, editing software, adobe |
is listed by: SoftCite is related to: Adobe Photoshop Lightroom |
SCR_014234, SCR_014298, SciRes_000161, SCR_002078 | http://www.adobe.com/products/cs6.html | SCR_014199 | Adobe Photoshop CC, Adobe Photoshop CS, Photoshop | 2026-09-03 04:52:30 | 26261 | ||||||||
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Origin Resource Report Resource Website 10000+ mentions |
Origin (RRID:SCR_014212) | data analysis software, data processing software, data visualization software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 4, 2025.Software application for data analysis and graphing. Origin contains a variety of different graph types, including statistical plots, 2D and 3D vector graphs, and counter graphs. More advance version is OriginPro which offers advanced analysis tools and Apps for Peak Fitting, Surface Fitting, Statistics and Signal Processing. | data, analysis, software, authoring, tool, scripting, graphing, statistical, publication |
is listed by: SoftCite is related to: OriginPro |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015636 | https://www.originlab.com/index.aspx?go=PRODUCTS&PID=1834 | SCR_014212 | OriginPro | 2026-09-03 04:52:38 | 13985 | |||||||
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Refmac Resource Report Resource Website 1000+ mentions |
Refmac (RRID:SCR_014225) | data analysis software, data processing software, sequence analysis software, software application, software resource | A molecular refinement program with two main modes: REVIEW, which checks and updates the input model to establish that the geometric restraints can be properly set up, and REFINE mode, which is the standard mode and documented in keywords. In REVIEW users can: check model coordinates and write an extended output set of coordinates, find disulphide bonds and other covalent links, cis-peptides, output the sequence and REMARK records. In REFINEMENT mode users can carry out rigid body, tls, restrained or unrestrained refinement against Xray data, or idealisation of a macromolecular structure. Also in REFINEMENT mode, Refmac produces an MTZ output file containing weighted coefficients for SigmaA weighted mFo-DFcalc and 2mFo-DFcalc maps. The program is supported by CCP4. | molecular refinement, data analysis software, sequence analysis software |
is used by: PDB-REDO is listed by: SoftCite |
SCR_014225 | 2026-09-03 04:52:38 | 2011 |
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