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Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability 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. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information.
| Version: | 2.4-5 |
| Depends: | R (≥ 3.1.0) |
| Imports: | Rcpp, parallel, grid, graphics, grDevices, stats, utils |
| LinkingTo: | Rcpp |
| Suggests: | XML, RCurl, lattice, ncdf4, igraph, bigmemory, knitr, rmarkdown, testthat (≥ 0.9.1), httr, msa, Biostrings |
| Published: | 2024-10-29 |
| DOI: | 10.32614/CRAN.package.bio3d |
| Author: | Barry Grant [aut, cre], Xin-Qiu Yao [aut], Lars Skjaerven [aut], Julien Ide [aut] |
| Maintainer: | Barry Grant <bjgrant at ucsd.edu> |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| URL: | http://thegrantlab.org/bio3d/, https://bitbucket.org/Grantlab/bio3d/ |
| NeedsCompilation: | yes |
| Citation: | bio3d citation info |
| Materials: | README NEWS |
| In views: | Omics |
| CRAN checks: | bio3d results |
| Reference manual: | bio3d.pdf |
| Vignettes: |
bio3d Vignettes (source) |
| Package source: | bio3d_2.4-5.tar.gz |
| Windows binaries: | r-devel: bio3d_2.4-5.zip, r-release: bio3d_2.4-5.zip, r-oldrel: bio3d_2.4-5.zip |
| macOS binaries: | r-release (arm64): bio3d_2.4-5.tgz, r-oldrel (arm64): bio3d_2.4-5.tgz, r-release (x86_64): bio3d_2.4-5.tgz, r-oldrel (x86_64): bio3d_2.4-5.tgz |
| Old sources: | bio3d archive |
| Reverse depends: | Bios2cor |
| Reverse imports: | aLFQ, compas, EnvNJ, orthGS, ptm, r3dmol, rPDBapi, SOMMD |
| Reverse suggests: | AlphaMissenseR, factR |
Please use the canonical form https://CRAN.R-project.org/package=bio3d to link to this page.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.