Package: pgxRpi 1.3.0

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_1.3.0.tar.gz
pgxRpi_1.3.0.zip(r-4.5)pgxRpi_1.3.0.zip(r-4.4)pgxRpi_1.3.0.zip(r-4.3)
pgxRpi_1.3.0.tgz(r-4.4-any)pgxRpi_1.3.0.tgz(r-4.3-any)
pgxRpi_1.3.0.tar.gz(r-4.5-noble)pgxRpi_1.3.0.tar.gz(r-4.4-noble)
pgxRpi_1.3.0.tgz(r-4.4-emscripten)pgxRpi_1.3.0.tgz(r-4.3-emscripten)
pgxRpi.pdf |pgxRpi.html✨
pgxRpi/json (API)
NEWS

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

Peer review:

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-1.1.11(bioc 3.20)pgxRpi-1.0.5(bioc 3.19)

copynumbervariationgenomicvariationdataimportsoftware

6.30 score 3 stars 21 scripts 130 downloads 6 exports 127 dependencies

Last updated 23 days agofrom:b85b31a3b1. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 31 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winNOTEOct 31 2024
R-4.4-macNOTEOct 31 2024
R-4.3-winNOTEOct 31 2024
R-4.3-macNOTEOct 31 2024

Exports:pgxFilterpgxFreqplotpgxLoaderpgxMetaplotpgxSegprocesssegtoFreq

Dependencies:abindaskpassattemptbackportsBiobaseBiocGenericsbootbroomcarcarDatacirclizeclicodetoolscolorspacecommonmarkcorrplotcowplotcpp11crayoncurldata.tableDelayedArrayDerivdigestdoBydplyrevaluateexactRankTestsfansifarverFormulafuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggpubrggrepelggsciggsignifggtextGlobalOptionsglobalsgluegridExtragridtextgtablehighrhttrIRangesisobandjpegjsonlitekm.ciKMsurvknitrlabelinglatticelifecyclelistenvlme4lubridatemagrittrmarkdownMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmaxstatmgcvmicrobenchmarkmimeminqamodelrmunsellmvtnormnlmenloptrnnetnumDerivopensslparallellypbkrtestpillarpkgconfigpngpolynompurrrquantregR6RColorBrewerRcppRcppEigenrlangrstatixS4ArraysS4VectorsscalesshapeSparseArraySparseMstringistringrSummarizedExperimentsurvivalsurvminersurvMiscsystibbletidyrtidyselecttimechangeUCSC.utilsutf8vctrsviridisLitewithrxfunxml2xtableXVectoryamlzlibbioczoo

Introduction_1_loadmetadata

Hangjia Zhao

Rendered fromIntroduction_1_loadmetadata.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-10-11
Started: 2023-06-14

Introduction_2_loadvariants

Hangjia Zhao

Rendered fromIntroduction_2_loadvariants.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-09-11
Started: 2023-06-14

Introduction_3_loadfrequency

Hangjia Zhao

Rendered fromIntroduction_3_loadfrequency.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-10-11
Started: 2023-06-14

Introduction_4_process_pgxseg

Hangjia Zhao

Rendered fromIntroduction_4_process_pgxseg.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-10-11
Started: 2023-06-14