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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CRAN Resource Report Resource Website 5000+ mentions |
CRAN (RRID:SCR_003005) | CRAN | software resource, software repository | 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 | 2026-08-02 09:03:31 | 5947 | |||||||
|
RankAggreg Resource Report Resource Website 10+ mentions |
RankAggreg (RRID:SCR_002225) | software resource | Software package that performs aggregation of ordered lists based on the ranks using several different algorithms: Borda count, Cross-Entropy Monte Carlo algorithm, Genetic algorithm, and a brute force algorithm. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:19228411 | GNU Lesser General Public License, v2, v2.1, v3 | OMICS_03526 | SCR_002225 | RankAggreg: Weighted rank aggregation | 2026-08-01 12:02:01 | 48 | |||||||
|
Iterative Signature Algorithm Resource Report Resource Website |
Iterative Signature Algorithm (RRID:SCR_002327) | isa2, ISA | software resource | A biclustering algorithm that finds modules in an input matrix. A module or bicluster is a block of the reordered input matrix. | standalone software, mac os x, unix/linux, windows, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: CRAN |
PMID:12689096 | Creative Commons Attribution-NonCommercial-ShareAlike License, v3 | biotools:isa, OMICS_03487 | https://bio.tools/isa | SCR_002327 | isa2: The Iterative Signature Algorithm | 2026-08-01 12:02:09 | 0 | |||||
|
Kdetrees Resource Report Resource Website |
Kdetrees (RRID:SCR_004522) | software resource | R package using a non-parametric method for estimating distributions of phylogenetic trees, with the goal of identifying trees that are significantly different from the rest of the trees in the sample. | applet, mac os x, unix/linux, windows, r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: CRAN |
PMID:24764459 | GNU General Public License, v2 | biotools:kdetrees, OMICS_04172 | https://github.com/grady/kdetrees, https://bio.tools/kdetrees | SCR_004522 | kdetrees: Nonparametric method for identifying discordant phylogenetic trees | 2026-08-01 12:02:40 | 0 | ||||||
|
ExomeDepth Resource Report Resource Website 100+ mentions |
ExomeDepth (RRID:SCR_002663) | software resource | Software that calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. | software package, unix/linux, mac os x, windows, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: CRAN |
PMID:22942019 | Free, Available for download, Freely available | OMICS_05443, biotools:exomedepth | https://bio.tools/exomedepth | SCR_002663 | 2026-08-01 12:01:52 | 262 | |||||||
|
FisHiCal Resource Report Resource Website |
FisHiCal (RRID:SCR_002799) | software resource | Software that integrates Hi-C and FISH data, offering a modular and easy-to-use tool for chromosomal spatial analysis. | standalone software, software package, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:25061071 | Free, Freely available, Available for download | OMICS_05207 | SCR_002799 | FisHiCal: Iterative FISH-based Calibration of Hi-C Data | 2026-08-01 12:02:13 | 0 | |||||||
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pairheatmap Resource Report Resource Website |
pairheatmap (RRID:SCR_003109) | software resource | A software tool to compare two heatmaps and discover patterns within and across groups. In the context of biology, group can be defined based on gene ontology. | standalone software, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: CRAN |
PMID:24016862 | Free, Available for download, Freely available | biotools:pairheatmap, OMICS_04853 | https://www.rdocumentation.org/packages/pairheatmap/versions/1.0.1/topics/pairheatmap | SCR_003109 | pairheatmap: A tool for comparing heatmaps | 2026-08-01 12:02:02 | 0 | ||||||
|
enviPat Resource Report Resource Website 10+ mentions |
enviPat (RRID:SCR_003034) | software resource | Software for fast and very memory-efficient calculation of isotope patterns, subsequent convolution to theoretical envelopes (profiles) plus valley detection and centroidization or intensoid calculation. Batch processing, resolution interpolation, wrapper, adduct calculations and molecular formula parsing. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
Free, Freely available | OMICS_02408 | SCR_003034 | enviPat: Isotope pattern profile and centroid calculation for mass spectrometry | 2026-08-01 12:02:24 | 27 | ||||||||
|
MCMC.qpcr Resource Report Resource Website 10+ mentions |
MCMC.qpcr (RRID:SCR_001721) | software resource | Software package that implements generalized linear mixed model analysis of qRT-PCR data based on lognormal-Poisson model fitted using MCMC. Control genes are not required but can be incorporated as Bayesian priors or, when template abundances correlate with conditions, as trackers of global effects (common to all genes). Also implemented are the lognormal model for higher-abundance data and a classic model involving multi-gene normalization on a by-sample basis. Several plotting functions are included to extract and visualize results. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:23977043 | Free, Available for download, Freely available | OMICS_03934 | SCR_001721 | MCMC.qpcr: Bayesian analysis of qRT-PCR data | 2026-08-01 12:02:00 | 24 | |||||||
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MetaDE Resource Report Resource Website 1+ mentions |
MetaDE (RRID:SCR_000199) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30, 2022. Software package that implements 12 major meta-analysis methods for differential expression analysis.Package was removed from the CRAN repository.Formerly available versions can be obtained from the archive.Archived on 2018-01-23 as check problems were not corrected in time. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:22863766 | Free, Available for download, Freely available | OMICS_04033 | http://cran.r-project.org/web/packages/MetaDE/ | SCR_000199 | MetaDE: Microarray meta-analysis for differentially expressed gene detection | 2026-08-01 12:01:09 | 1 | ||||||
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aLFQ Resource Report Resource Website 10+ mentions |
aLFQ (RRID:SCR_005925) | software resource | An R-package for estimating absolute protein quantities from label-free liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics data. It supports the commonly used absolute label-free protein abundance estimation methods (TopN, iBAQ, APEX, NSAF and SCAMPI) for LC-MS/MS proteomics data, quantifying on either MS1-, MS2-levels or spectral counts together with validation algorithms to enable automated data analysis and error estimation. Specifically, they used Monte-carlo cross-validation and bootstrapping for model selection and imputation of proteome-wide absolute protein quantity estimation. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:24753486 | GNU General Public License, v3 or greater | OMICS_04053 | SCR_005925 | aLFQ: An R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data | 2026-08-01 12:03:01 | 22 | |||||||
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YuGene Resource Report Resource Website 10+ mentions |
YuGene (RRID:SCR_006023) | software resource | Software providing a simple method for comparison of gene expression generated across different experiments, and on different platforms; that does not require global renormalization, and is not restricted to comparison of identical probes. YuGene works on a range of microarray dataset distributions, such as between manufacturers. The resulting output allows direct comparisons of gene expression between experiments and experimental platforms. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:24667244 | GNU General Public License, v2, v3 | OMICS_04030 | SCR_006023 | YuGene: A simple approach to scale gene expression data derived from different platforms for integrated analyses | 2026-08-01 12:03:03 | 13 | |||||||
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R package inTrees Resource Report Resource Website 1+ mentions |
R package inTrees (RRID:SCR_017299) | software toolkit, software resource | Software R package for tree ensembles such as random forests, regularized random forests and gradient boosted trees. Provides functions for extracting, measuring and pruning rules, selecting compact rule set, summarizing rules into learner, calculating frequent variable interactions, formatting rules in latex code. | tree, ensemble, random, forest, gradient, extracting, function, measuring, pruning, formatting, variable, interaction, latex, code | has parent organization: CRAN | Free, Available for download, Freely available | https://github.com/softwaredeng/inTrees/issues | SCR_017299 | inTrees | 2026-08-02 09:07:47 | 2 | ||||||||
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ggplot2 Resource Report Resource Website 10000+ mentions |
ggplot2 (RRID:SCR_014601) | data processing software, data visualization software, software application, software resource | Open source software package for statistical programming language R to create plots based on grammar of graphics. Used for data visualization to break up graphs into semantic components such as scales and layers. | plotting system, r, graphics, data analysis, multi-layered graphics, bio.tools |
uses: ggpubr uses: ggeffects uses: ggsignif is used by: riboWaltz is used by: ClustVis is used by: ggrepel is used by: PlotsOfData is used by: EnhancedVolcano is used by: tidyverse is used by: ComplexUpset is used by: ggfortify is used by: forestmodel is used by: ggvenn is used by: metaviz is used by: ggVennDiagram is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing is related to: ggraph is related to: ggbiplot is related to: GGally is related to: ggstatsplot has parent organization: CRAN works with: Plotly works with: cowplot works with: ggalluvial works with: ggforce works with: ggbreak works with: ggrastr works with: tidybayes works with: ggsurvfit works with: ggtext works with: ggsci |
Free, Freely available | biotools:ggplot2 | http://docs.ggplot2.org/current/, https://github.com/tidyverse/ggplot2, https://bio.tools/ggplot2 | http://ggplot2.org/ | SCR_014601 | grammar of graphics plot2 | 2026-08-04 09:43:29 | 36105 | ||||||
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ggrepel Resource Report Resource Website 50+ mentions |
ggrepel (RRID:SCR_017393) | software application, standalone software, software resource | Software tool to provide text and label geoms for ggplot2 that help to avoid overlapping text labels. Labels repel away from each other and away from data points. | text, label, geoms, avoid, overlapping |
uses: ggplot2 is used by: EnhancedVolcano has parent organization: CRAN |
Free, Available for download, Freely available | https://github.com/slowkow/ggrepel | SCR_017393 | 2026-08-04 09:44:08 | 50 | |||||||||
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aCGH.Spline Resource Report Resource Website |
aCGH.Spline (RRID:SCR_002927) | software resource | An R package for array comparative genomic hybridization (aCGH) dye bias normalization. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:21357574 | Free, Available for download, Freely available | OMICS_02607 | http://cran.r-project.org/web/packages/aCGH.Spline/ | SCR_002927 | 2026-08-01 12:02:21 | 0 | |||||||
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CNVassoc Resource Report Resource Website 1+ mentions |
CNVassoc (RRID:SCR_002901) | software resource | Software package that carries out association analysis of common copy number variants in population-based studies. It includes functions for analysing association under a series of study designs (case-control, cohort, etc), using several dependent variables (class status, censored data, counts) as response, adjusting for covariates and considering various inheritance models. It also includes functions for inferring copy number (CNV genotype calling). Various classes and methods for generic functions (print, summary, plot, anova, ... ) have been created to facilitate the analysis. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:21609482 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02609 | SCR_002901 | CNVassoc: Association analysis of CNV data | 2026-08-01 12:01:57 | 1 | |||||||
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Isopat Resource Report Resource Website |
Isopat (RRID:SCR_003025) | software resource | Software function that calculates the isotopic pattern (fine structures) for a given chemical formula. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
Free, Available for download, Freely available | OMICS_02409 | https://isopat.sourceforge.net/ | SCR_003025 | isopat: Calculation of isotopic pattern for a given molecular formula | 2026-08-01 12:02:24 | 0 | |||||||
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Parametric Time Warping Resource Report Resource Website |
Parametric Time Warping (RRID:SCR_003053) | ptw | software resource | Software that aligns patterns, i.e. it aims to put corresponding features at the same locations. The algorithm searches for an optimal polynomial describing the warping. It is possible to align one sample to a reference, several samples to the same reference, or several samples to several references. One can choose between calculating individual warpings, or one global warping for a set of samples and one reference. Two optimization criteria are implemented: RMS (Root Mean Square error) and WCC (Weighted Cross Correlation). | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:14719890 | Free, Freely available | OMICS_02392 | SCR_003053 | ptw: Parametric Time Warping | 2026-08-01 12:02:01 | 0 | ||||||
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RCircos Resource Report Resource Website 100+ mentions |
RCircos (RRID:SCR_003310) | software resource | Software package that provides a simple and flexible way to generate Circos 2D track plot images for genomic data visualization. The types of plots include: heatmap, histogram, lines, scatterplot, tiles and plot items for further decorations include connector, link (lines and ribbons), and text (gene) label. All functions require only R graphics package that comes with R base installation. | standalone software, unix/linux, mac os x, windows, r |
is listed by: OMICtools is related to: shinyCircoss has parent organization: CRAN has parent organization: Bitbucket |
PMID:23937229 | Free, Available for download, Freely available | OMICS_04661 | https://bitbucket.org/henryhzhang/rcircos/ | SCR_003310 | RCircos: Circos 2D Track Plot | 2026-08-01 12:02:29 | 245 |
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