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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://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   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/shazam/index.html

Software R package provides computational framework for analyzing mutations in immunoglobulin sequences. Immunoglobulin Somatic Hypermutation Analysis.

Proper citation: shazam (RRID:SCR_024301) 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://dendropy.org/

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   

•   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://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   

•   Source: SciCrunch Registry

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   

•   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

http://edwards.sdsu.edu/cgi-bin/prinseq/prinseq.cgi

A publicly available tool that is able to filter, reformat and trim your genomic and metagenomic sequence data and provide you summary statistics for your sequence data. The interactive web interface facilitates visualizations of the results and export functionality for subsequent data processing. The standalone lite version is written in Perl and does not require any non-core Perl modules. The lite version is primarily designed for data preprocessing and does not generate summary statistics in graphical form., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PRINSEQ (RRID:SCR_005454) Copy   

•   Source: SciCrunch Registry

http://www.tmanavigator.org/

A free web-based service open to all users for analysis of tissue microarray (TMA) data and related information, accommodating categorical, semi-continuous and continuous expression scores. There is no login requirement.

Proper citation: TMA Navigator (RRID:SCR_005599) Copy   

•   Source: SciCrunch Registry