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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://www.rostlab.org/owiki/index.php/Norsnet

Software as neural network based method that focuses on identification of unstructured loops. Trained to distinguish between very long contiguous segments with non-regular secondary structure and well-folded proteins. Trained on predicted information rather than on experimental data.

Proper citation: NORSnet (RRID:SCR_024146) Copy   

•   Source: SciCrunch Registry

http://www.opensurgsim.org/

Open source software framework that includes the necessary building blocks for surgical simulations, such as native device support, haptic feedback, graphics, discrete collision detection and physics simulation. Developers can refactor the physics engine, swap models, ODE solvers, or linear system solvers.

Proper citation: OpenSurgSim (RRID:SCR_024147) 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

http://openigtlink.org/

Open source software network communication interface for image guided interventions.Provides plug-and-play unified real-time communications in operating rooms for image-guided interventions, where imagers, sensors, surgical robots,and computers from different vendors work cooperatively to ensure seamless data flow among those components and enable a closed loop process of planning, control, delivery, and feedback.

Proper citation: OpenIGTLink (RRID:SCR_024148) 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://psignifit.sourceforge.net/

Software toolbox to fit psychometric functions and to test hypotheses about psychometric data.

Proper citation: psignifit (RRID:SCR_024196) 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

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

Software R package for interfacing with BIOM format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, limited support for writing biom-object back to biom-format file.

Proper citation: biomformat (RRID:SCR_024228) Copy   

•   Source: SciCrunch Registry

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

Software R package to provide set of utilities, color schemes and conventions for genomic data. Used for various high-level packages for biological data visualization.

Proper citation: biovizBase (RRID:SCR_024229) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/data/annotation/html/GO.db.html

Software R package provides set of annotation maps describing entire Gene Ontology assembled using data from GO.

Proper citation: go.db (RRID:SCR_024241) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/impute/

Software R package for imputation for microarray data.

Proper citation: impute (RRID:SCR_024243) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/Mergeomics/

Software R pacakage for multidimensional data integration to identify pathogenic perturbations to biological systems. Used for integrating multidimensional omics disease associations, functional genomics, canonical pathways and gene-gene interaction networks to generate mechanistic hypotheses. Includes Marker set enrichment analysis and Weighted Key Driver Analysis parts.

Proper citation: mergeomics (RRID:SCR_024244) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/metagenomeSeq/

Software R package to determine features that are differentially abundant between two or more groups of multiple samples. Used to address the effects of both normalization and under-sampling of microbial communities on disease association detection and testing of feature correlations.

Proper citation: metagenomeseq (RRID:SCR_024246) Copy   

•   Source: SciCrunch Registry