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https://cran.r-project.org/package=parmigene

Software R package for parallel estimation of mutual information based on entropy estimates from k-nearest neighbors distances and algorithms for reconstruction of gene regulatory networks.

Proper citation: parmigene (RRID:SCR_024285) Copy   

•   Source: SciCrunch Registry

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

Software R package provides functions for principal component analysis by projection pursuit.

Proper citation: pcapp (RRID:SCR_024287) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/package=psychotree

Software R package for recursive partitioning based on psychometric models, employing general MOB algorithm to obtain Bradley-Terry trees, Rasch trees, rating scale and partial credit trees, and MPT trees, trees for 1PL, 2PL, 3PL and 4PL models and generalized partial credit models.

Proper citation: psychotree (RRID:SCR_024288) Copy   

•   Source: SciCrunch Registry

http://saint-apms.sourceforge.net/Main.html

Software package for assigning confidence scores to protein-protein interactions based on quantitative proteomics data in AP-MS experiments.

Proper citation: saint (RRID:SCR_024324) Copy   

•   Source: SciCrunch Registry

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

Software R package contains methods for detection of clusters in hierarchical clustering dendrograms.

Proper citation: dynamicTreeCut (RRID:SCR_024280) Copy   

•   Source: SciCrunch Registry

https://github.com/artic-network/readucks

Software package as Nanopore read de-multiplexer.

Proper citation: readucks (RRID:SCR_024315) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/package=stringi

Software R package as collection of character string/text/natural language processing tools for pattern searching, random string generation, case mapping, string transliteration, concatenation, sorting, padding, wrapping, Unicode normalisation, date time formatting and parsing.

Proper citation: stringi (RRID:SCR_024319) Copy   

•   Source: SciCrunch Registry

http://varna.lri.fr/

Software tool for automated drawing, visualization and annotation of secondary structure of RNA, designed as companion software for web servers and databases.Allows manual modification and structural annotation of resulting drawing using either interactive point and click approach, within web server or through command-line arguments.

Proper citation: VARNA (RRID:SCR_024373) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/preprocessCore/

Software library of core preprocessing routines.

Proper citation: preprocesscore (RRID:SCR_024254) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/qusage/

Software R package is implementation Quantitative Set Analysis for Gene Expression method. Used to provide faster, more accurate, and easier to understand test for gene expression studies.

Proper citation: qusage (RRID:SCR_024255) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/Rsamtools/

Software R package provides interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating Sequence Alignment Map, FASTA, binary variant call and compressed indexed tab-delimited files.

Proper citation: rsamtools (RRID:SCR_024257) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/savR/

Software R package to parse Illumina Sequence Analysis Viewer files, access data, and generate QC plots.

Proper citation: savr (RRID:SCR_024258) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/NanoStringQCPro/

Software R package to assess quality of NanoString mRNA gene expression data, to identify outlier probes and outlier samples. Provides different background subtraction and normalization approaches for this data. It outputs suggestions for flagging samples/probes and easily sharable html quality control output.

Proper citation: nanostringqcpro (RRID:SCR_024250) Copy   

•   Source: SciCrunch Registry

https://github.com/vgteam/vg#vg

Software toolkit to improve read mapping by representing genetic variation in reference.Provides succinct encoding of sequences of many genomes.

Proper citation: variation graph (RRID:SCR_024369) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/PWMEnrich/

Software toolkit of high level functions for DNA motif scanning and enrichment analysis built upon Biostrings. Used for PWM enrichment analysis of already known PWMs. Also implements high-level functions for PWM scanning and visualisation.

Proper citation: pwmenrich (RRID:SCR_024249) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/XVector/

Software R package provides memory efficient S4 classes for storing sequences externally.

Proper citation: xvector (RRID:SCR_024263) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/trinculo/

Software toolkit for carrying out genetic association for multi-catagory phenotypes. Implements multinomial and ordinal association incorporating covariates, conditional analysis, empirical and non-emperical priors and fine-mapping.

Proper citation: Trinculo (RRID:SCR_024384) Copy   

•   Source: SciCrunch Registry

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

Software R package provides functions to reconstruct, generate, and simulate synchronous, asynchronous, probabilistic, and temporal Boolean networks. Provides also functions to analyze and visualize attractors in Boolean networks.

Proper citation: BoolNet (RRID:SCR_024264) Copy   

•   Source: SciCrunch Registry

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

Software R package for estimation, testing and regression modeling of subdistribution functions in competing risks.

Proper citation: cmprsk (RRID:SCR_024265) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/bio3d/index.html

Softwar R package for comparative analysis of protein structures. Used to process, organize and explore protein structure, sequence and dynamics data. Used to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. Enables statistical and graphical power of R environment to work with biological sequence and structural data.

Proper citation: bio3d (RRID:SCR_024266) Copy   

•   Source: SciCrunch Registry