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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   

•   Source: SciCrunch Registry

https://github.com/BIMSBbioinfo/pigx_rnaseq

Software reproducible genomics analysis pipelines with GNU Guix. Used for analysis of RNA sequencing, chromatin immunoprecipitation sequencing, bisulfite-treated DNA sequencing, and single-cell resolution RNA sequencing. All pipelines process raw experimental data and generate reports containing publication-ready plots and figures, with interactive report elements and standard observables.

Proper citation: PiGx-RNAseq (RRID:SCR_024160) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/geneplotter/

Software R package provides functions for plotting genomic data

Proper citation: geneplotter (RRID:SCR_024234) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/HTSFilter/

Software R package implements filtering procedure for replicated transcriptome sequencing data based on global Jaccard similarity index in order to identify genes with low, constant levels of expression across one or more experimental conditions.

Proper citation: htsfilter (RRID:SCR_024242) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/MultiAssayExperiment.html

Software R package to harmonize data management of multiple experimental assays performed on overlapping set of specimens.Provides user experience by extending concepts from SummarizedExperiment, supporting open-ended mix of standard data classes for individual assays, and allowing subsetting by genomic ranges or rownames. Facilities are provided for reshaping data into wide and long formats for adaptability to graphing and downstream analysis.

Proper citation: multiassayexperiment (RRID:SCR_024245) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/MutationalPatterns.html

Software R package provides set of flexible functions to evaluate and visualize multitude of mutational patterns in base substitution catalogues of e.g. healthy samples, tumour samples, or DNA-repair deficient cells.

Proper citation: mutationalpatterns (RRID:SCR_024247) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/groHMM/

Software R package for analysis of GRO-seq data. Used for identifying unannotated and cell type-specific transcription units from global run-on sequencing data

Proper citation: groHMM (RRID:SCR_024237) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/genefilter/

Software R package provides some basic functions for filtering genes.

Proper citation: genefilter (RRID:SCR_024238) Copy   

•   Source: SciCrunch Registry