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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://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://github.com/rrwick/Unicycler

Software assembly pipeline for bacterial genomes. Used for resolving bacterial genome assemblies from short and long sequencing reads. Can assemble Illumina only read sets where it functions as SPAdes-optimiser. Can assembly long read only sets for PacBio or Nanopore where it runs miniasm+Racon pipeline.

Proper citation: Unicycler (RRID:SCR_024380) 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/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://tab2mage.sourceforge.net/

Software package written and supported by ArrayExpress curation team, which aims to ease the process of submitting large microarray experiment datasets to our public repository database.

Proper citation: tab2mage (RRID:SCR_024359) Copy   

•   Source: SciCrunch Registry

http://www.uhnresearch.ca/labs/tillier/ProDesign/ProDesign.html

Webserver that can be used to find oligonucleotide probe sets for microarray slides. The probes can be for individual sequences or for clusters of genes. This webserver accepts files up to 200 kb in size in order to minimize the running time. For larger files please download the program.

Proper citation: ProDesign (RRID:SCR_010966) Copy   

•   Source: SciCrunch Registry

http://kmersvm.beerlab.org/

A webserver built on the Galaxy framework that enables the mining of sequence data for transcription factor binding sites. This tool suite was designed to aid in analysis of next-generation sequencing (NGS) data that uses a support vector machine (SVM) with kmer sequence features to identify predictive combinations of short transcription factor binding sites which determine the tissue specificity of the original NGS assay. While you may use datasets already available from Galaxy, you can upload your data using the ''Get Data'' Tool. The tool can upload data from a variety of locations.

Proper citation: kmer-SVM (RRID:SCR_010882) Copy   

•   Source: SciCrunch Registry

http://ccb.jhu.edu/software/glimmer/index.shtml

A software system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.

Proper citation: Glimmer (RRID:SCR_011931) Copy   

•   Source: SciCrunch Registry