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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/mroosmalen/nanosv

Software package that can be used to identify structural genomic variations in long-read sequencing data, such as data produced by Oxford Nanopore Technologies� MinION, GridION or PromethION instruments, or Pacific Biosciences RSII or Sequel sequencers.

Proper citation: NanoSV (RRID:SCR_024127) 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://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

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

Software R package provides functions for design and analysis of dose finding experiments. Used for multiple contrast tests, fitting non-linear dose-response models, calculating optimal designs and implementation of MCPMod methodology.

Proper citation: DoseFinding (RRID:SCR_024268) Copy   

•   Source: SciCrunch Registry

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

Software R package for geodesic distance between phylogenetic trees and associated functions.

Proper citation: distory (RRID:SCR_024269) Copy   

•   Source: SciCrunch Registry

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

Software R package for high-throughput adaptive immune receptor repertoire sequencing analysis. In particular, immunoglobulin sequence lineage reconstruction, lineage topology analysis, diversity profiling, amino acid property analysis and gene usage.

Proper citation: alakazam (RRID:SCR_024261) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/ade4/index.html

Software R package for multivariate data analysis. Used for analysis of one-table, two-table, three-table and K-table.

Proper citation: ade4 (RRID:SCR_024259) Copy   

•   Source: SciCrunch Registry

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

Software R pacakge provides functions and load identifier mapping databases in R. Uses GitHub, Zenodo, and Figshare if you use this package to download identifier mappings files.

Proper citation: bridgedbr (RRID:SCR_024231) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/CNEr/

Software R package provides large scale identification and advanced visualization of sets of conserved noncoding elements.

Proper citation: CNEr (RRID:SCR_024233) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/GenomeInfoDb/

Software R package contains data and functions that define and allow translation between different chromosome sequence naming conventions, including function that attempts to place sequence names in their natural, rather than lexicographic order.

Proper citation: genomeinfodb (RRID:SCR_024235) Copy   

•   Source: SciCrunch Registry

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

Software R package provides efficient containers for storing and manipulating short genomic alignments. This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.

Proper citation: genomicalignments (RRID:SCR_024236) Copy   

•   Source: SciCrunch Registry

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

Software R package defines many S4 generic functions used in Bioconductor.

Proper citation: BiocGenerics (RRID:SCR_024226) Copy   

•   Source: SciCrunch Registry