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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Definiens Developer XD Resource Report Resource Website 10+ mentions |
Definiens Developer XD (RRID:SCR_014283) | software resource | A development environment designed to create automated image analysis solutions for segmentation and classification tasks. It delivers quantitative and consistent data for any type of image (e.g., IHC, ISH, IF images in different formats). Developer XD also contains a large library of image analysis algorithms, which users can add to, for whole slide images and tissue microarrays (TMAs). It can be integrated with an existing Tissue Studio installation. | development environment, image analysis solution, segmentation, classification, image analysis algorithm library, tissue microarray, whole slide image, tissue studio | is listed by: SoftCite | SCR_014283 | 2026-09-12 12:58:15 | 11 | |||||||||||
|
I-TASSER Resource Report Resource Website 1000+ mentions |
I-TASSER (RRID:SCR_014627) | data analysis software, data processing software, software application, software resource | Web server as integrated platform for automated protein structure and function prediction. Used for protein 3D structure prediction. Resource for automated protein structure prediction and structure-based function annotation. | Automated prediction, protein structure prediction, protein function prediction, protein 3D structure, amino acid sequence, alignment, simulation, 3D atomic model, protein, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: University of Michigan; Ann Arbor; USA has parent organization: University of Kansas; Kansas; USA |
NIGMS GM083107; NIGMS GM084222 |
DOI:10.1186/1471-2105-9-40 DOI:10.1093/nar/gkv342 PMID:20360767 PMID:18215316 |
Free, Available for download, Freely available | biotools:i-tasser, SCR_018803 | https://bio.tools/i-tasser | SCR_014627 | Iterative Threading Assembly Refinement, Iterative Threading ASSEmbly Refinement | 2026-09-12 12:58:19 | 3874 | |||||
|
Cufflinks Resource Report Resource Website 5000+ mentions |
Cufflinks (RRID:SCR_014597) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for transcriptome assembly and differential expression analysis for RNA-Seq. Includes script called cuffmerge that can be used to merge together several Cufflinks assemblies. It also handles running Cuffcompare as well as automatically filtering a number of transfrags that are likely to be artifacts. If the researcher has a reference GTF file, the researcher can provide it to the script to more effectively merge novel isoforms and maximize overall assembly quality. | transcriptome, rna-seq, rna seq, cuffmerge, cufflink, cuffcompare, transfrags, artifacts, gtf file, transcriptome assembly, expression analysis, bio.tools, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite works with: GeneScissors is hosted by: GitHub |
DOI:10.1038/nbt.1621 | Acknowledgement requested, Source code available on GitHub | biotools:cufflinks, OMICS_01304, SCR_013307 | https://github.com/cole-trapnell-lab/cufflinks, https://bio.tools/cufflinks, https://sources.debian.org/src/cufflinks/ | SCR_014597 | 2026-09-12 12:58:19 | 9083 | |||||||
|
COMSOL Multiphysics Resource Report Resource Website 50+ mentions |
COMSOL Multiphysics (RRID:SCR_014767) | simulation software, software application, software resource | General-purpose software platform for modeling and simulating physics-based problems which accounts for coupled or multiphysics phenomena. The platform includes a set of core physics interfaces for common physics application areas such as structural analysis, laminar flow, pressure acoustics, transport of diluted species, electrostatics, electric currents, heat transfer, and Joule heating. | simulation software, software platform, physics, problem solver | is listed by: SoftCite | Commercially available | SCR_014767 | 2026-09-12 12:58:21 | 51 | ||||||||||
|
CVODE Resource Report Resource Website 50+ mentions |
CVODE (RRID:SCR_014696) | data analysis software, data processing software, software application, software resource | Solver for stiff and nonstiff ordinary differential equation (ODE) systems (initial value problem), given in explicit form y' = f(t,y), based on Adams and BDF methods. It is one of the programs that makes up the Suite of Nonlinear and Differential/Algebraic Equation Solvers (SUNDIALS)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | data analysis software, solver, equation solver, ordinary differential equation, differential equation, stiff, nonstiff | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014696 | SUNDIALS CVODE | 2026-09-12 12:58:20 | 56 | |||||||||
|
ELDA Resource Report Resource Website 100+ mentions |
ELDA (RRID:SCR_018933) | analysis service resource, data analysis software, data processing software, production service resource, service resource, software application, software resource | Software tool for limiting dilution analysis, with particular attention to needs of stem cell assays. Provides confidence intervals for all LDA data sets, including those with 0% or 100% responses. Other features include test of adequacy of single hit hypothesis, tests for frequency differences between multiple data sets, and ability to take advantage of cases where number of cells in sample is counted exactly. | Limiting dilution analysis, stem cell assay, data set confidence intervals, single hit hypothesis, adequacy test, frequency differences test | is listed by: SoftCite | PMID:19567251 | Free, Freely available | SCR_018933 | Extreme Limiting Dilution Analysis | 2026-09-12 12:59:07 | 463 | ||||||||
|
PROCHECK Resource Report Resource Website 100+ mentions |
PROCHECK (RRID:SCR_019043) | data analysis software, data processing software, software application, software resource | Software tool to check stereochemical quality of protein structures. Its outputs comprise number of plots in PostScript format and comprehensive residue by residue listing. Includes PROCHECK-NMR for checking quality of structures solved by NMR. | Stereochemical quality, protein structure, plot, residue listing, protein, assessing protein quality, | is listed by: SoftCite | DOI:10.1107/S0021889892009944 | Free, Available for download | SCR_019043 | 2026-09-12 12:59:09 | 122 | |||||||||
|
igraph Resource Report Resource Website 100+ mentions |
igraph (RRID:SCR_019225) | data analysis software, data processing software, data visualization software, network analysis software, network graph visualization software, software application, software resource, software toolkit | Software package for graphs and network analysis. Provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.Can be programmed in R, Python, Mathematica, C/C Plus Plus. | Graphs analysis, network analysis, generating graph function, graph visualization |
is listed by: CRAN is listed by: SoftCite is related to: igraph for R |
Free, Available for download, Freely available | https://igraph.org/, https://github.com/igraph/igraph/releases/tag/0.8.4 | SCR_019225 | igraph 0.8.4, igraph 1.2.6 | 2026-09-12 12:59:11 | 432 | ||||||||
|
OpenClinica Resource Report Resource Website 10+ mentions |
OpenClinica (RRID:SCR_019223) | data acquisition software, data processing software, software application, software resource | Web platform for electronic data capture by OpenClinica, LLC. Used as clinical trial management system. | Clinical trial, data management system, clinical trial management system, clinical data, clinical data management | is listed by: SoftCite | PMID:21893916 | Restricted | https://www.openclinica.com/community-edition-open-source-edc/ | SCR_019223 | 2026-09-12 12:59:11 | 46 | ||||||||
|
Integrative Genomics Viewer Resource Report Resource Website 500+ mentions |
Integrative Genomics Viewer (RRID:SCR_011793) | IGV | software resource | A high-performance visualization tool for interactive exploration of large, integrated genomic datasets. | genomic datasets exploration, |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Broad Institute |
DOI:10.1038/nbt.1754 | OMICS_00917, biotools:igv | https://bio.tools/igv, https://sources.debian.org/src/igv/ | SCR_011793 | 2026-09-12 12:57:39 | 878 | |||||||
|
CANGS Resource Report Resource Website 1+ mentions |
CANGS (RRID:SCR_011837) | CANGS | data analysis software, data processing software, software application, software resource | A user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies. | windows, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
PMID:20180949 | biotools:cangs, OMICS_01084 | https://bio.tools/cangs | SCR_011837 | 2026-09-12 12:57:40 | 1 | |||||||
|
Prodigal Resource Report Resource Website 1000+ mentions |
Prodigal (RRID:SCR_011936) | Prodigal | simulation software, software application, software resource | Software tool for protein coding gene prediction for prokaryotic genomes. |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite has parent organization: Oak Ridge National Laboratory |
PMID:20211023 | Free, Available for download, Freely available | SCR_021246, OMICS_01493 | https://sources.debian.org/src/prodigal/ | http://prodigal.ornl.gov/ | SCR_011936 | , PROkaryotic DYnamic programming Gene-finding ALgorithm, Prokaryotic Dynamic Programming Genefinding Algorithm | 2026-09-12 12:57:42 | 3398 | |||||
|
Genesis Resource Report Resource Website 1000+ mentions |
Genesis (RRID:SCR_015775) | data analysis software, data processing software, data visualization software, software application, software resource | Software for cluster analysis of microarray data. Genesis is a platform independent Java package of tools to simultaneously visualize and analyze a whole set of gene expression experiments. | cluster analysis, microarray data, java, gene expression, visualization, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
PMID:11836235 | Free for academic use, Free for non-profits, Available for download, Runs on Windows, Runs on Mac OS, Runs on Linux | biotools:genesis_microarray | https://bio.tools/genesis_microarray | SCR_015775 | Genesis: Cluster analysis of microarray data | 2026-09-12 12:58:30 | 1029 | ||||||
|
Gblocks Resource Report Resource Website 1000+ mentions |
Gblocks (RRID:SCR_015945) | software application, software resource, standalone software, web application | Software that eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | position, dna, protein, align, alignment, phylogenetic, analysis, block, ansi c, deletion, removal | is listed by: SoftCite | Desarrollo e Innovación Tecnológica ; Fundación BBVA ; Plan Nacional de Investigación Científica BIO2002-04426-C02-02 |
PMID:10742046 PMID:17654362 |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015945 | 2026-09-12 12:58:32 | 2043 | ||||||||
|
AMBER Resource Report Resource Website 1000+ mentions |
AMBER (RRID:SCR_016151) | AMBER | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | Software toolkit for the comparative assessment of genome reconstructions from metagenome benchmark datasets. It provides performance metrics, results rankings, and comparative visualizations for assessing multiple programs or parameter effects. | binning, metagenomics, benchmarking, biobox, evaluation, comparison, reconstruction, metric, |
is used by: CHARMM-GUI is listed by: SoftCite |
DOI:10.1101/239582 | Free, Available for download | SCR_016151 | AMBER: Assessment of Metagenome BinnERs | 2026-09-12 12:58:36 | 2205 | |||||||
|
FCS Express Resource Report Resource Website 500+ mentions |
FCS Express (RRID:SCR_016431) | data analysis software, data processing software, software application, software resource | Software tool for flow and image cytometry data analysis by De Novo Software company. | flow, image, analysis, data, cytometry, De Novo Software, research, clinical, laboratory | is listed by: SoftCite | Commercially available, Tutorial available | SCR_016431 | 2026-09-12 12:58:39 | 518 | ||||||||||
|
MedCalc Resource Report Resource Website 10000+ mentions |
MedCalc (RRID:SCR_015044) | data analysis software, data processing software, software application, software resource | Statistical software for ROC curve analysis. MedCalc performs several statistical tests such as method comparison, method evaluation, reference intervals, and meta-analysis. | statistic, statistical analysis, roc curve, reference software | is listed by: SoftCite | Commercially available, Available for purchase, Trial available | SCR_015044 | 2026-09-12 12:58:24 | 19712 | ||||||||||
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KaleidaGraph Resource Report Resource Website 1000+ mentions |
KaleidaGraph (RRID:SCR_014980) | data analysis software, data processing software, data visualization software, software application, software resource | Data analysis, graphing, and management application that allows users to import, manipulate, analyze data, and create customized plots. Plots include x-y probability, histogram, box, percentile, horizontal bar, stack bar, column, stack column, polar, and pie. Binned data can be exported to a histogram, step plot, or spike plot. KaleidaGraph works with Windows and Macintosh systems., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | custom graph, custom plot, publishable graph, publishable plot, data manipulation, curve fitting | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014980 | 2026-09-12 12:58:24 | 2789 | ||||||||||
|
BoxPlotR Resource Report Resource Website 100+ mentions |
BoxPlotR (RRID:SCR_015629) | data processing software, data visualization software, software application, software resource, web application | Web tool written in R for generation of box plots with R packages shiny, beanplot4, vioplot, beeswarm and RColorBrewer, and hosted on shiny server to allow for interactive data analysis. Data are held temporarily and discarded as soon as session terminates.Represents both summary statistics and distribution of primary data. Enables visualization of minimum, lower quartile, median, upper quartile and maximum of any data set.Data matrix can be uploaded as file or pasted into application. May be downloaded to run locally or as virtual machine for VMware and VirtualBox. | Box plot generation, customized box plot, data, plot, analysis |
is listed by: SoftCite is related to: PlotsOfData is related to: vioplot |
ERC ; Genome Québec International Recruitment Award ; Wellcome Trust ; WTCCB |
PMID:24481215 | Free, Available for download, Freely available | SCR_018327 | https://github.com/VizWizard/BoxPlotR.shiny | SCR_015629 | 2026-09-12 12:58:28 | 370 | ||||||
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oligo Resource Report Resource Website 1000+ mentions |
oligo (RRID:SCR_015729) | data analysis software, data processing software, software application, software resource, source code | Software package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files). | oligonucleotide, microarray gene expression, r, oligonucleotide array, snp, gene expression, probe-level, affymetrix array, cel file, and nimblegen array, xys file, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
CAPES (Coordenação de Aprimoramento Pessoal de Nível Superior) ; NCRR R01RR021967; NHGRI P41HG004059 |
PMID:20688976 | Free, Available for download, Runs on Mac OS, Runs on Windows | biotools:oligo | https://bio.tools/oligo | SCR_015729 | oligo package | 2026-09-12 12:58:29 | 1808 |
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