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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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HMPTrees Resource Report Resource Website |
HMPTrees (RRID:SCR_014613) | data analysis software, data processing software, software application, software resource | An R-package which uses Object Oriented Data Analysis (OODA) methods to analyze taxonomic trees directly, providing tools to model, compare, and visualize populations of taxonomic tree objects. | microbiome, r, taxonomic tree, rdp, statistical object oriented data | is listed by: Human Microbiome Project | SCR_014613 | Statistical Object Oriented Data Analysis of RDP-Based Taxonomic Trees from Human Microbiome Data, HMPTrees - Statistical Object Oriented Data Analysis of RDP-Based Taxonomic Trees from Human Microbiome Data | 2026-09-12 12:58:19 | 0 | ||||||||||
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CTSgetR Resource Report Resource Website |
CTSgetR (RRID:SCR_014672) | software application, software resource, source code, systems interoperability software | R interface to Chemical Translation Service which provides translation between chemical and biological database identifiers. | statistical analysis, statistical analysis package, r, r package, source code, system interoperability, software, translation, chemical, metabolomics | is listed by: Metabolomics Workbench | Freely available | SCR_014672 | 2026-09-12 12:58:20 | 0 | ||||||||||
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kruX Resource Report Resource Website 1+ mentions |
kruX (RRID:SCR_012076) | software resource | An algorithm implemented in Matlab, Python and R that uses matrix multiplications to simultaneously calculate the Kruskal-Wallis test statistic for several millions of marker-trait combinations at once. | standalone software, matlab, python, r |
is listed by: OMICtools has parent organization: Google Code |
PMID:24423115 | GNU General Public License | OMICS_04593 | SCR_012076 | 2026-09-12 12:57:44 | 5 | ||||||||
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xMSanalyzer Resource Report Resource Website 50+ mentions |
xMSanalyzer (RRID:SCR_012144) | software resource | A software package of utilities for data extraction, quality control assessment, detection of overlapping and unique metabolites in multiple datasets, and batch annotation of metabolites. xMSanalyzer comprises of utilities that can be classified into five main modules: 1) merging apLCMS or XCMS sample processing results from multiple sets of parameter settings, 2) evaluation of sample quality, feature consistency, and batch-effect, 3) feature matching, and 4) characterization of m/z using KEGG REST; 5) Batch-effect correction using ComBat. | software package, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23323971 | GNU General Public License | OMICS_06039 | SCR_012144 | 2026-09-12 12:57:46 | 90 | ||||||||
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PICS Resource Report Resource Website 1+ mentions |
PICS (RRID:SCR_001093) | data analysis software, data processing software, sequence analysis software, software application, software resource | R package with tools that use probabilistic inference of ChIP-Seq. It follows an empirical Bayes mixture model approach. | chip seq, bayes, data, r, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
PMID:20528864 | Free, Available for download, Freely available | OMICS_00455 | SCR_001093 | Probabilistic inference of ChIP-seq | 2026-09-12 01:00:07 | 3 | |||||||
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R-package for adaptive fMRI analysis Resource Report Resource Website |
R-package for adaptive fMRI analysis (RRID:SCR_002530) | R-package for adaptive fMRI analysis | data processing software, image analysis software, image processing software, software application, software resource | The package fmri provides fMRI analysis with R using structural adaptive smoothing methods. They allow smoothing especially at low SNR avoiding the apparent blurring of non-adapative smoothing and thus without reducing the effective spatial resolution. | afni brik, analyze, console (text based), dicom, fortran, macos, microsoft, magnetic resonance, nifti, posix/unix-like, r, fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center |
Free | nlx_155935 | SCR_002530 | 2026-09-12 01:00:08 | 0 | ||||||||
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Synapse Resource Report Resource Website 1000+ mentions |
Synapse (RRID:SCR_006307) | Synapse | data or information resource, data repository, database, service resource, storage service resource | A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data. | data sharing, collaboration, data management, analysis, genome, phenotype, crowd sourcing, open data, provenance, resource management, annotation, authoring, markup, r, python, java, command-line, cloud, FASEB list |
is used by: NF Data Portal is listed by: FORCE11 is listed by: DataCite is listed by: re3data.org is related to: clearScience is related to: Exemplar Microscopy Images of Tissues has parent organization: Sage Bionetworks |
Cancer, Normal, Cardiovascular disease, Floppy hat syndrome | Life Sciences Discovery Fund ; NCI ; NHLBI ; Alfred P. Sloan Foundation |
The community can contribute to this resource | nlx_151983, DOI:10.17616/R3B934, r3d100011894, DOI:10.7303 | https://doi.org/10.17616/R3B934, https://doi.org/10.48550/arxiv.1506.00272, https://doi.org/10.7303/, https://dx.doi.org/10.7303, https://doi.org/10.17616/R3B934 | SCR_006307 | 2026-09-12 01:00:12 | 1104 | |||||
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rstatix Resource Report Resource Website 100+ mentions |
rstatix (RRID:SCR_021240) | data analytics software, software application, software resource, software toolkit | Software R package for basic statistical tests including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and correlation analyses. Output of each test is automatically transformed into data frame to facilitate visualization. Additional functions are available for reshaping, reordering, manipulating and visualizing correlation matrix. Functions are also included to facilitate analysis of factorial experiments. Can compute several effect size metrics.Package contains helper functions for identifying univariate and multivariate outliers, assessing normality and homogeneity of variances. | Statistical tests, t-test, Wilcoxon test, ANOVA, Kruskal-Wallis, correlation analyses, R, visualization | is listed by: CRAN | Free, Available for download, Freely available | https://github.com/kassambara/rstatix | SCR_021240 | 2026-09-12 12:59:53 | 133 | |||||||||
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LDHEATMAP Resource Report Resource Website 100+ mentions |
LDHEATMAP (RRID:SCR_006312) | software application, software resource | Software application that plots measures of pairwise linkage disequilibria for SNPs (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | nlx_154424, SCR_009347, nlx_154561 | http://stat-db.stat.sfu.ca:8080/statgen/research/LDheatmap | SCR_006312 | R/LDHEATMAP | 2026-09-12 01:00:56 | 169 | ||||||||
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HCLUST Resource Report Resource Website 1000+ mentions |
HCLUST (RRID:SCR_009154) | HCLUST | software application, software resource | Software application that is a simple clustering method that can be used to rapidly identify a set of tag SNP's based upon genotype data (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, r, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:h-clust, SCR_009102, nlx_154195, nlx_154331 | https://bio.tools/h-clust | SCR_009154 | R/HCLUST | 2026-09-12 01:00:59 | 1460 | ||||||
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ReadqPCR Resource Report Resource Website |
ReadqPCR (RRID:SCR_000030) | software application, software resource, standalone software | A software package that provides functions to read raw RT-qPCR data of different platforms. | standalone software, mac os x, unix/linux, windows, r, data import, gene expression, microtitre plate assay, qpcr, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor has parent organization: University College London; London; United Kingdom |
PMID:22748112 | Free, Available for download, Freely available | biotools:readqpcr, OMICS_03936 | https://bio.tools/readqpcr | SCR_000030 | ReadqPCR - Read qPCR data | 2026-09-12 01:02:22 | 0 | ||||||
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Database Enabled Code for Ideal Probe Hybridization Employing R Resource Report Resource Website 1+ mentions |
Database Enabled Code for Ideal Probe Hybridization Employing R (RRID:SCR_000581) | DECIPHER | software resource, software toolkit | A software toolset that can be used for deciphering and managing DNA sequences efficiently using the R statistical programming language., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | 16s rrna sequence, chimera, primer, probe, array, 16s oligo, dna sequence, r |
is listed by: OMICtools has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
PMID:22101057 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01114 | SCR_000581 | 2026-09-12 01:02:23 | 2 | |||||||
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Shiny Resource Report Resource Website 500+ mentions |
Shiny (RRID:SCR_001626) | software resource, software toolkit | Open source R package that provides web framework for building web applications using R. Used to create interactive web apps in native R, without needing to use HTML, CSS, or JavaScript. | R, analysis, interactive, web, application |
uses: shinythemes is used by: ClustVis is used by: shinyGEO is used by: PlotsOfData is used by: shinyCircoss is used by: AlloMate is used by: VenomView is used by: bulkAnalyseR is related to: rSPRITE is related to: EHRtemporalVariability is related to: robvis is related to: Omics Data Paper Generator is related to: Mitochondrial Neuron Ubiquitin is related to: chevreul is related to: Click-qPCR is related to: EMImR is related to: Mona has parent organization: RStudio works with: BoxPlotR works with: shinyhelper works with: ShinyCell works with: Breedverse works with: GenoBrew |
PMID:34642739 PMID:26225240 |
Free, Available for download, Freely available | nlx_153894 | SCR_001626 | 2026-09-12 01:02:26 | 590 | ||||||||
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CAROL Resource Report Resource Website 10+ mentions |
CAROL (RRID:SCR_001800) | CAROL | software application, software resource | Software application that is a combined functional annotation score of non-synonymous coding variants. A major challenge in interpreting whole-exome data is predicting which of the discovered variants are deleterious or neutral. To address this question in silico, they have developed a score called Combined Annotation scoRing toOL (CAROL), which combines information from two bioinformatics tools: PolyPhen-2 and SIFT, in order to improve the prediction of the effect of non-synonymous coding variants. The combination of annotation tools can help improve automated prediction of whole-genome/exome non-synonymous variant functional consequences. (entry from Genetic Analysis Software) The software should run on any UNIX or GNU/Linux system. | gene, genetic, genomic, r, prediction, non-synonymous coding variant |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:22261837 | Free, Available for download, Freely available | nlx_154254, OMICS_00143 | http://www.sanger.ac.uk/resources/software/carol/ | SCR_001800 | Combined Annotation scoRing toOL | 2026-09-12 01:02:26 | 11 | |||||
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CRAN Resource Report Resource Website 5000+ mentions |
CRAN (RRID:SCR_003005) | CRAN | software repository, software resource | Network of ftp and web servers around world that store identical, up to date, versions of code and documentation for R. Package archive network for R programming language. | network, ftp, web, server, code, documentation, mirror, R |
lists: lme4 lists: R package: nlme lists: R package: lmerTest lists: R package: RVAideMemoire lists: R package: LMERConvenienceFunctions lists: R package: psy lists: R package: lattice lists: geomorph lists: Sequenza lists: NeuroAnatomy Toolbox lists: dplyr lists: Prophet lists: metagear lists: tidyr lists: Mediation Analysis of Causality under Confounding lists: MIIVsem lists: rjags lists: GENEPOP lists: webchem lists: cowplot lists: readxl lists: biomod2 lists: multcomp lists: knitr lists: ggtree lists: Minimum-Hypergeometric Test lists: meta lists: Network-Based R-Statistics lists: pavo lists: Modern Applied Statistics with S lists: cvequality lists: openxlsx lists: tidyverse lists: Genomic Annotation in Livestock for positional candidate LOci lists: igraph lists: SIMR lists: gbs2ploidy lists: vioplot lists: spdep lists: maps lists: Differential Gene Correlation Analysis lists: ez lists: celltrackR lists: rentrez lists: pepr lists: survival lists: ggpubr lists: Signac lists: rstatix lists: ggalluvial lists: purrr lists: gtsummary lists: questionr lists: powereQTL lists: RSurveillance lists: epiR lists: psych lists: CCP lists: yacca lists: DHARMa lists: Companion to Applied Regression lists: Peptides lists: taxize lists: seqinr lists: reshape2 lists: mvabund lists: CpGassoc lists: metaMA lists: ComplexUpset lists: eulerr lists: shinyhelper lists: shinythemes lists: philentropy lists: lwgeom lists: stringr lists: ordinal lists: msigdbr lists: meta4diag lists: Rtrack lists: ggsignif lists: Corrplot lists: immunarch lists: Algorithms and Framework for Nonnegative Matrix Factorization lists: Computing Chance Corrected Agreement Coefficients lists: Intraclass Correlations for Quantifying Inter Rater Reliability lists: Regression Modeling Strategies lists: caret lists: AICcmodavg lists: RHRV lists: FFTrees lists: Simple Features lists: rworldmap lists: eHDprep lists: vcfR lists: vtree lists: SimplyAgree lists: randomizeR lists: DiagrammeR lists: forestplot lists: merTools lists: clusterSim lists: bibliometrix lists: Rtsne lists: brms lists: oncoPredict lists: epitools lists: DrugSim2DR lists: rstanarm lists: scCustomize lists: corrplot lists: Parsnip lists: ggbreak lists: FactoMineR lists: tidycmprsk lists: BioCircos lists: Matrix based Flexible Project Planning is affiliated with: R Project for Statistical Computing is affiliated with: factoextra is affiliated with: dendsort is affiliated with: viridis is affiliated with: RColorBrewer is affiliated with: statmod is affiliated with: ANOCVA is related to: flowBin is related to: CorMut is related to: VariantAnnotation is related to: timecourse is related to: RmiR.Hs.miRNA is related to: PSCBS is related to: sybil - Efficient Constrained Based Modelling in R is related to: categoryCompare is related to: clValid is related to: pheatmap is related to: RaceID is related to: BRASS is related to: IDR is related to: ascend is related to: brainGraph is related to: GBM R package is related to: Phangorn is related to: ape is related to: missForest is related to: trend is related to: precrec is related to: EHRtemporalVariability is related to: emmeans is related to: reshape is related to: variancePartition is related to: SimFFPE is related to: FilterFFPE is related to: shinyCircoss is related to: Betareg is related to: ggeffects is related to: Harrell Miscellaneous is related to: simplePHENOTYPES is related to: Bayesian Generalized Linear Regression is related to: ranger is related to: h2o4gpu is related to: ridge regression Best Linear Unbiased Prediction is related to: Classification And Regression Training is related to: ggforce is related to: janitor is related to: Rphenograph is parent organization of: Postgwas is parent organization of: MetaDE is parent organization of: MCMC.qpcr is parent organization of: PurBayes is parent organization of: circlize is parent organization of: neuRosim is parent organization of: metaRNASeq is parent organization of: RankAggreg is parent organization of: DEMI is parent organization of: Iterative Signature Algorithm is parent organization of: MUMA is parent organization of: VennDiagram is parent organization of: ExomeDepth is parent organization of: FisHiCal is parent organization of: CNVassoc is parent organization of: aCGH.Spline is parent organization of: Isopat is parent organization of: enviPat is parent organization of: Parametric Time Warping is parent organization of: enviPick is parent organization of: pairheatmap is parent organization of: RCircos is parent organization of: MultiPhen is parent organization of: aLFQ is parent organization of: MetaQC is parent organization of: YuGene is parent organization of: Kdetrees is parent organization of: ggplot2 is parent organization of: R package inTrees is parent organization of: ggrepel hosts: MSM |
nif-0000-30270 | http://cran.r-project.org/mirrors.html | SCR_003005 | the Comprehensive R Archive Network, Comprehensive R Archive Network, The Comprehensive R Archive Network | 2026-09-12 01:02:29 | 7039 | |||||||
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CPRDLooksups.R Resource Report Resource Website |
CPRDLooksups.R (RRID:SCR_018959) | software application, software resource, text extraction software | Software R tool used to identify and retrieve CPRD clinical additional record information such as, smoking, weight/BMI, and medical tests. | Script, R, identify information, retrieve information, CPRD, clinical record information, smoking, weight, BMI, medical test, clinical data | Free, Freely available | SCR_018959 | 2026-09-12 01:02:19 | 0 | |||||||||||
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POPGEN Resource Report Resource Website 100+ mentions |
POPGEN (RRID:SCR_007315) | software application, software resource | An R package that specifically focuses on statistical and population genetics methods. The motivation behind the package is to produce an easy to use interface to many of the commonly used methods and models used in statistical and population genetics and an alternative interface for some of the methodology produced by our group. (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | nlx_154543, SCR_009374, nlx_154596 | http://mathgen.stats.ox.ac.uk/software.html, https://cran.r-project.org/web/packages/popgen/index.html | SCR_007315 | R/POPGEN | 2026-09-12 01:02:36 | 205 | ||||||||
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SNP-HWE Resource Report Resource Website 1+ mentions |
SNP-HWE (RRID:SCR_008555) | SNP-HWE | software application, software resource | Software application for a fast exact Hardy-Weinberg Equilibrium test for SNPs (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran, c, c++, r | is listed by: Genetic Analysis Software | nlx_154645 | SCR_008555 | 2026-09-12 01:02:38 | 4 | |||||||||
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ModelMaker Resource Report Resource Website 10+ mentions |
ModelMaker (RRID:SCR_009024) | ModelMaker | software application, software resource | Multi-threaded, parallel and CUDA based application that provides an interface to the R statistical language, MATLAB, Accord and Aforge APIs, along with Neural Maestro to accomplish fMRI, EEG, speech signals, commodity price analysis, general machine learning, classification and time series analysis and forecasting. Because it unifies research development work in MATLAB, R and C++, it provides a mathematical canvas the permits researches to experiment with both pure and hybrid models that use the best of all software development languages. | fmri, eeg, speech signal, commodity price analysis, machine learning, classification, time series analysis, forecasting, time series, r, matlab |
is related to: iBIOFind is related to: Neural Maestro has parent organization: The Cromwell Workshop |
Request required | nlx_153828 | http://neuronalarchitects.com/model-maker.html | SCR_009024 | Model Maker | 2026-09-12 01:02:38 | 17 | ||||||
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R/META Resource Report Resource Website 50+ mentions |
R/META (RRID:SCR_009175) | R/META | software application, software resource | Software application for fixed and random effects meta-analysis. Functions for tests of bias, forest and funnel plot. (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | nlx_154307 | SCR_009175 | 2026-09-12 01:02:41 | 65 |
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