Package: GrafGen 1.9.0

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_1.9.0.tar.gz
GrafGen_1.9.0.zip(r-4.7)GrafGen_1.9.0.zip(r-4.6)GrafGen_1.9.0.zip(r-4.5)
GrafGen_1.9.0.tgz(r-4.6-x86_64)GrafGen_1.9.0.tgz(r-4.6-arm64)GrafGen_1.9.0.tgz(r-4.5-x86_64)GrafGen_1.9.0.tgz(r-4.5-arm64)
GrafGen_1.9.0.tar.gz(r-4.7-arm64)GrafGen_1.9.0.tar.gz(r-4.7-x86_64)GrafGen_1.9.0.tar.gz(r-4.6-arm64)GrafGen_1.9.0.tar.gz(r-4.6-x86_64)
GrafGen_1.9.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GrafGen/json (API)

# 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:

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

On BioConductor:GrafGen-1.9.0(bioc 3.24)GrafGen-1.8.0(bioc 3.23)

genetics software genomeannotation classification cpp

4.18 score 2 scripts 5 exports 120 dependencies

Last updated from:12ab634014. Checks:1 NOTE, 9 OK, 4 WARNING. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	245
linux-devel-arm64	OK	237
linux-devel-x86_64	OK	347
source / vignettes	OK	261
linux-release-arm64	OK	246
linux-release-x86_64	OK	281
macos-release-arm64	WARNING	122
macos-release-x86_64	WARNING	227
macos-oldrel-arm64	WARNING	151
macos-oldrel-x86_64	WARNING	258
windows-devel	OK	234
windows-release	OK	182
windows-oldrel	OK	197
wasm-release	OK	207

Exports:createApp grafGen grafGenPlot interactivePlot interactiveReferencePlot

Dependencies:abind askpass backports base64enc BiocGenerics boot broom bslib cachem car carData cli colorspace commonmark corrplot cowplot cpp11 crosstalk curl data.table Deriv digest doBy dplyr evaluate farver fastmap fontawesome forecast Formula fracdiff fs generics 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 lmtest magrittr MASS Matrix MatrixModels memoise mgcv mime minqa modelr nlme nloptr nnet numDeriv openssl otel pbkrtest pillar pkgconfig plotly polynom promises purrr quantreg R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas rlang rmarkdown rstatix S4Vectors S7 sass scales Seqinfo shiny sourcetools SparseM stringi stringr survival sys tibble tidyr tidyselect timeDate tinytex urca utf8 vctrs viridisLite withr xfun xtable yaml zoo

GrafGen: Classifying Subpopulations of H. pylori Genomes

Rendered fromvignette.Rmdusingknitr::rmarkdown

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