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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
https://bioconductor.org/packages/release/bioc/html/ctc.html
Software R package for export and import classification trees and clusters to other programs.
Proper citation: ctc (RRID:SCR_024232) Copy
https://bioconductor.org/packages/geneplotter/
Software R package provides functions for plotting genomic data
Proper citation: geneplotter (RRID:SCR_024234) Copy
https://github.com/cogent3/cogent3
Software Python library for analysis of genomic sequence data. Framework for novel probabilistic analyses of biological sequences, devising workflows, and generating publication quality graphics.
Proper citation: PyCogent (RRID:SCR_024192) Copy
https://github.com/open2c/cooler
Software library for sparse, compressed, binary persistent storage format used to store genomic interaction data, such as Hi-C contact matrices.Scalable storage for Hi-C data and other genomically labeled arrays.
Proper citation: Cooler (RRID:SCR_024194) Copy
https://bioconductor.org/packages/release/bioc/html/AnnotationHub.html
Software R package to provide a client for the Bioconductor AnnotationHub web resource. AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered.
Proper citation: AnnotationHub (RRID:SCR_024227) Copy
https://bioconductor.org/packages/hypergraph/
Software R package that implements some simple capabilities for representing and manipulating hypergraphs.
Proper citation: hypergraph (RRID:SCR_024240) Copy
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