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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://cran.r-project.org/web/packages/DT/index.html
Software R package for data objects in R to render as HTML tables using JavaScript library DataTables. DataTables library has been included in this R package.
Proper citation: DT (RRID:SCR_024270) Copy
https://cran.r-project.org/web/packages/NMF/index.html
Software R package provides framework to perform Non-negative Matrix Factorization.Used for nonnegative matrix factorization.Implements set of already published algorithms and seeding methods, and provides framework to test, develop and plug new/custom algorithms. Most of the built-in algorithms have been optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines.
Proper citation: nmf (RRID:SCR_024284) Copy
https://cran.r-project.org/package=pROC
Software R tools for visualizing, smoothing and comparing receiver operating characteristic. Partial area under curve AUC can be compared with statistical tests based on U-statistics or bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.
Proper citation: proc (RRID:SCR_024286) Copy
https://qtltools.github.io/qtltools/
Software tool set for molecular Quantitative Trait Loci discovery and analysis. Allows to go from raw sequence data to collection of molecular Quantitative Trait Loci in few easy-to-perform steps.
Proper citation: qtltools (RRID:SCR_024200) Copy
https://cran.r-project.org/package=psyphy
Software R package useful in analyzing data from psychophysical experiments.Includes functions for calculating d' from several different experimental designs, links for m-alternative forced-choice data to be used with binomial family in glm and self-Start functions for estimating gamma values for CRT screen calibrations.
Proper citation: psyphy (RRID:SCR_024289) Copy
https://gitlab.com/RKIBioinformaticsPipelines/QCumber
Software for quality control, quality trimming, adapter removal and sequence content check of NGS data.
Proper citation: qcumber (RRID:SCR_024203) Copy
https://cran.r-project.org/web/packages/Mediana/index.html
Software R package for clinical trial simulations based on Clinical Scenario Evaluation approach. The package supports broad class of data models, analysis strategies and commonly used evaluation criteria.
Proper citation: mediana (RRID:SCR_024281) Copy
https://cran.r-project.org/web/packages/itertools/index.html
Software R package for creating iterators, many patterned after functions in the Python itertools module, and others patterned after functions in the 'snow' package.
Proper citation: itertools (RRID:SCR_024282) Copy
https://cran.r-project.org/web/packages/OptimalCutpoints/index.html
Software R package to compute optimal cutpoints for diagnostic tests or continuous markers.Used for selecting optimal cutoffs, analysis and diagnostic test accuracy measures.
Proper citation: optimalcutpoints (RRID:SCR_024283) Copy
https://bioconductor.org/packages/RBGL/
Software R package as interface to the graph algorithms contained in the BOOST library.
Proper citation: rbgl (RRID:SCR_024251) Copy
https://bioconductor.org/packages/release/bioc/html/pcaMethods.html
Software R package providing PCA methods for incomplete data. Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and conventional SVD PCA. Cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation.
Proper citation: pcaMethods (RRID:SCR_024252) Copy
https://bioconductor.org/packages/Rcpi/
Software R package as molecular informatics toolkit with integration of bioinformatics and chemoinformatics tools for drug discovery.
Proper citation: rcpi (RRID:SCR_024253) Copy
https://bioconductor.org/packages/release/bioc/html/rgsepd.html
Software R package to help disambiguate transcriptome samples by automating differential expression, then gene set enrichment, and finally N-dimensional projection to quantify in which ways each sample is like either treatment group.
Proper citation: rgsepd (RRID:SCR_024256) Copy
https://bioconductor.org/packages/makecdfenv/
Software R package has two functions. One reads Affymetrix chip description file and creates hash table environment containing location/probe set membership mapping. The other creates package that automatically loads that environment.
Proper citation: makecdfenv (RRID:SCR_024248) Copy
https://cran.r-project.org/web/packages/beeswarm/index.html
Software R package implementing bee swarm plots. Bee swarm plot is one-dimensional scatter plot like "stripchart", but with closely packed, non overlapping points.
Proper citation: beeswarm (RRID:SCR_024262) Copy
https://cran.r-project.org/web/packages/adephylo/index.html
Software R package provides multivariate tools to analyze comparative data. Analysis of comparative evolutionary data. Used for investigating phylogenetic signal in biological traits.
Proper citation: adephylo (RRID:SCR_024267) Copy
https://cran.r-project.org/web/packages/rpact/index.html
Software R package for design and analysis of confirmatory adaptive clinical trials with continuous, binary, and survival endpoints.
Proper citation: rpact (RRID:SCR_024300) Copy
https://bioconductor.org/packages/TFBSTools/
Software R package for analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software.
Proper citation: tfbstools (RRID:SCR_024260) Copy
Software Python library for phylogenetic computing. Provides classes and functions for simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in range of formats, such as NEXUS, NEWICK, NeXML, Phylip, FASTA., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: DendroPy (RRID:SCR_024197) Copy
https://bioconductor.org/packages/BSgenome/
Software R package provides infrastructure shared by all the Biostrings-based genome data packages.
Proper citation: bsgenome (RRID:SCR_024230) Copy
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