Package: pgxRpi 1.8.0

Hangjia Zhao

pgxRpi: R wrapper for Progenetix

The package is an R wrapper for Progenetix REST API built upon the Beacon v2 protocol. Its purpose is to provide a seamless way for retrieving genomic data from Progenetix database—an open resource dedicated to curated oncogenomic profiles. Empowered by this package, users can effortlessly access and visualize data from Progenetix.

Authors:Hangjia Zhao [aut, cre], Michael Baudis [aut]

pgxRpi_1.8.0.tar.gz
pgxRpi_1.8.0.zip(r-4.7-any)pgxRpi_1.8.0.zip(r-4.6-any)pgxRpi_1.8.0.zip(r-4.5-any)
pgxRpi_1.8.0.tgz(r-4.6-any)pgxRpi_1.8.0.tgz(r-4.5-any)
pgxRpi_1.8.0.tar.gz(r-4.7-any)pgxRpi_1.8.0.tar.gz(r-4.6-any)
pgxRpi_1.8.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
pgxRpi/json (API)

# Install 'pgxRpi' in R:

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

Bug tracker:https://github.com/progenetix/pgxrpi/issues

Datasets:

hg19_cytoband - A dataframe containing cytoband annotation details extracted from the hg19 gennome. It is used for CNV frequency visualization.
hg38_cytoband - A dataframe containing cytoband annotation details extracted from the hg38 gennome. It is used for CNV frequency visualization.

On BioConductor:pgxRpi-1.9.0(bioc 3.24)pgxRpi-1.7.0(bioc 3.23)

copynumbervariation genomicvariation dataimport software

3.65 score 3 stars 9 scripts 5 exports 123 dependencies

Last updated from:0f8693294a (on RELEASE_3_23). Checks:1 NOTE, 8 ERROR, 1 OK. Indexed: no.

Target	Result	Time
bioc-checks	NOTE	197
linux-devel-x86_64	ERROR	220
source / vignettes	ERROR	295
linux-release-x86_64	ERROR	199
macos-release-arm64	ERROR	91
macos-oldrel-arm64	ERROR	81
windows-devel	ERROR	103
windows-release	ERROR	108
windows-oldrel	ERROR	98
wasm-release	OK	171

Exports:pgxFreqplot pgxLoader pgxMetaplot pgxSegprocess segtoFreq

Dependencies:abind askpass attempt backports Biobase BiocGenerics boot broom car carData circlize cli codetools colorspace commonmark corrplot cowplot cpp11 curl DelayedArray Deriv digest doBy dplyr exactRankTests farver forecast Formula fracdiff future future.apply generics GenomicRanges ggplot2 ggpubr ggrepel ggsci ggsignif ggtext GlobalOptions globals glue gridExtra gridtext gtable httr IRanges isoband jpeg jsonlite labeling lattice lifecycle listenv litedown lme4 lmtest lubridate magrittr markdown MASS Matrix MatrixGenerics MatrixModels matrixStats maxstat mgcv mime minqa modelr mvtnorm nlme nloptr nnet numDeriv openssl parallelly pbkrtest pillar pkgconfig png polynom purrr quantreg R6 rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas rlang rstatix S4Arrays S4Vectors S7 scales Seqinfo shape SparseArray SparseM stringi stringr SummarizedExperiment survival survminer sys tibble tidyr tidyselect timechange timeDate urca utf8 vctrs viridisLite withr xfun xml2 XVector yaml zoo

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
A dataframe containing cytoband annotation details extracted from the hg19 gennome. It is used for CNV frequency visualization.	hg19_cytoband
A dataframe containing cytoband annotation details extracted from the hg38 gennome. It is used for CNV frequency visualization.	hg38_cytoband
Plot CNV frequency data	pgxFreqplot
Load data from Progenetix database via the Beacon v2 API with some extensions	pgxLoader
Plot survival data of individuals	pgxMetaplot
Extract, analyse and visualize "pgxseg" files	pgxSegprocess
Calculate CNV frequency data from given segment data	segtoFreq