Package: protein8k 0.0.1

protein8k: Perform Analysis and Create Visualizations of Proteins

Read Protein Data Bank (PDB) files, performs its analysis, and presents the result using different visualization types including 3D. The package also has additional capability for handling Virus Report data from the National Center for Biotechnology Information (NCBI) database.

Authors:Simon Liles

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protein8k.pdf |protein8k.html✨
protein8k/json (API)

# Install 'protein8k' in R:

install.packages('protein8k', repos = c('https://simonliles.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/simonliles/protein8k/issues

Datasets:

p53_tetramerization - P53 Tetramerization Domain Crystal Structure

On CRAN:

pdb protein protein-structure

4.00 score 1 stars 4 scripts 140 downloads 11 exports 65 dependencies

Last updated 4 years agofrom:4e97277448. Checks:3 OK, 5 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 05 2025
R-4.5-win	NOTE	Feb 05 2025
R-4.5-mac	NOTE	Feb 05 2025
R-4.5-linux	NOTE	Feb 05 2025
R-4.4-win	NOTE	Feb 05 2025
R-4.4-mac	NOTE	Feb 05 2025
R-4.3-win	OK	Feb 05 2025
R-4.3-mac	OK	Feb 05 2025

Exports:fromJSONL getAtomicRecord getTitleSection plot3D plotModels Protein3D read.pdb report_as_dataframe summary summary.Protein write_viz

Dependencies:base64enc bslib cachem cli codetools colorspace commonmark cpp11 crayon curl digest dplyr fansi farver fastmap fontawesome fs generics ggplot2 glue gridExtra gtable htmltools httpuv isoband jquerylib jsonlite labeling later lattice lifecycle lobstr magick magrittr MASS Matrix memoise mgcv mime munsell nlme pillar pkgconfig prettyunits promises pryr R6 rappdirs RColorBrewer Rcpp rjson rlang sass scales shiny sourcetools stringi stringr tibble tidyselect utf8 vctrs viridisLite withr xtable

Introduction to protein8k

Simon Liles

Rendered fromintro_protein8k.Rmdusingknitr::rmarkdownon Feb 05 2025.

Last update: 2021-04-24
Started: 2021-04-02

Using plot3D()

Simon Liles

Rendered fromusing_plot3D.Rmdusingknitr::rmarkdownon Feb 05 2025.

Last update: 2021-04-25
Started: 2021-04-25

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
fromJSONL	fromJSONL
getAtomicRecord	getAtomicRecord
getTitleSection	getTitleSection
P53 Tetramerization Domain Crystal Structure	p53_tetramerization
plot3D	plot3D
plotModels	plotModels
Protein Class Definitions	Protein-class
plot3DInteractive	Protein3D
read.pdb	read.pdb
report_as_dataframe	report_as_dataframe
summary.Protein	summary summary,Protein,ANY-method summary,Protein-method
summary.Protein	summary.Protein
write_viz	write_viz