Package: GrafGen 1.3.0

William Wheeler

GrafGen: Classification of Helicobacter Pylori Genomes

To classify Helicobacter pylori genomes according to genetic distance from nine reference populations. The nine reference populations are hpgpAfrica, hpgpAfrica-distant, hpgpAfroamerica, hpgpEuroamerica, hpgpMediterranea, hpgpEurope, hpgpEurasia, hpgpAsia, and hpgpAklavik86-like. The vertex populations are Africa, Europe and Asia.

Authors:William Wheeler [aut, cre], Difei Wang [aut], Isaac Zhao [aut], Yumi Jin [aut], Charles Rabkin [aut]

GrafGen_1.3.0.tar.gz
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GrafGen.pdf |GrafGen.html✨
GrafGen/json (API)
NEWS

# Install 'GrafGen' in R:

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

Bug tracker:https://github.com/wheelerb/grafgen/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

HpyloriData - H. pylori data
example_metadata - Metadata for examples
grafGen_example_results - Example results
grafGen_reference_dataframe - Reference data results for plots
grafGen_reference_results - Reference data results

On BioConductor:GrafGen-1.3.0(bioc 3.21)GrafGen-1.2.0(bioc 3.20)

genetics software genomeannotation classification cpp

4.65 score 2 scripts 132 downloads 5 exports 116 dependencies

Last updated 6 days agofrom:5d94ee825f. Checks:OK: 9. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 17 2024
R-4.5-win-x86_64	OK	Dec 03 2024
R-4.5-linux-x86_64	OK	Dec 17 2024
R-4.4-win-x86_64	OK	Dec 03 2024
R-4.4-mac-x86_64	OK	Dec 17 2024
R-4.4-mac-aarch64	OK	Dec 17 2024
R-4.3-win-x86_64	OK	Dec 03 2024
R-4.3-mac-x86_64	OK	Dec 17 2024
R-4.3-mac-aarch64	OK	Dec 17 2024

Exports:createApp grafGen grafGenPlot interactivePlot interactiveReferencePlot

Dependencies:abind askpass backports base64enc BiocGenerics boot broom bslib cachem car carData cli colorspace commonmark corrplot cowplot cpp11 crayon crosstalk curl data.table Deriv digest doBy dplyr evaluate fansi farver fastmap fontawesome Formula fs generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 ggpubr ggrepel ggsci ggsignif glue gridExtra gtable highr htmltools htmlwidgets httpuv httr IRanges isoband jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle lme4 magrittr MASS Matrix MatrixModels memoise mgcv microbenchmark mime minqa modelr munsell nlme nloptr nnet numDeriv openssl pbkrtest pillar pkgconfig plotly polynom promises purrr quantreg R6 rappdirs RColorBrewer Rcpp RcppEigen rlang rmarkdown rstatix S4Vectors sass scales shiny sourcetools SparseM stringi stringr survival sys tibble tidyr tidyselect tinytex UCSC.utils utf8 vctrs viridisLite withr xfun xtable XVector yaml zlibbioc

GrafGen: Classifying Subpopulations of H. pylori Genomes

William Wheeler, Difei Wang, Isaac Zhao, Yumi Jin and Charles Rabkin

Rendered fromvignette.Rmdusingknitr::rmarkdownon Dec 17 2024.

Last update: 2024-02-28
Started: 2024-01-17

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Classify H. pylori genomes	GrafGen-package GrafGen
R Shiny App	createApp
Metadata for examples	example_metadata
Reference population for H. pylori strains	grafGen
Example results	grafGen_example_results
Reference data results for plots	grafGen_reference_dataframe
Reference data results	grafGen_reference_results
Plot results	grafGenPlot
H. pylori data	HpyloriData
Interactive plot of user's data	interactivePlot
Interactive plot of the reference data	interactiveReferencePlot
Plot and Print	plot.grafpop print.grafpop