Package: pgxRpi 1.3.2

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_1.3.2.tar.gz
pgxRpi_1.3.2.zip(r-4.5)pgxRpi_1.3.2.zip(r-4.4)pgxRpi_1.3.2.zip(r-4.3)
pgxRpi_1.3.2.tgz(r-4.4-any)pgxRpi_1.3.2.tgz(r-4.3-any)
pgxRpi_1.3.2.tar.gz(r-4.5-noble)pgxRpi_1.3.2.tar.gz(r-4.4-noble)
pgxRpi_1.3.2.tgz(r-4.4-emscripten)pgxRpi_1.3.2.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-1.3.1(bioc 3.21)pgxRpi-1.2.0(bioc 3.20)

copynumbervariationgenomicvariationdataimportsoftware

6.28 score 3 stars 21 scripts 130 downloads 5 exports 129 dependencies

Last updated 15 days agofrom:2ead4cfdcf. Checks:1 OK, 6 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 18 2025
R-4.5-winERRORJan 18 2025
R-4.5-linuxERRORJan 18 2025
R-4.4-winERRORJan 18 2025
R-4.4-macERRORJan 18 2025
R-4.3-winERRORJan 18 2025
R-4.3-macERRORJan 18 2025

Exports:pgxFreqplotpgxLoaderpgxMetaplotpgxSegprocesssegtoFreq

Dependencies:abindaskpassattemptbackportsBiobaseBiocGenericsbootbroomcarcarDatacirclizeclicodetoolscolorspacecommonmarkcorrplotcowplotcpp11crayoncurldata.tableDelayedArrayDerivdigestdoBydplyrevaluateexactRankTestsfansifarverFormulafuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggpubrggrepelggsciggsignifggtextGlobalOptionsglobalsgluegridExtragridtextgtablehighrhttrIRangesisobandjpegjsonlitekm.ciKMsurvknitrlabelinglatticelifecyclelistenvlme4lubridatemagrittrmarkdownMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmaxstatmgcvmicrobenchmarkmimeminqamodelrmunsellmvtnormnlmenloptrnnetnumDerivopensslparallellypbkrtestpillarpkgconfigpngpolynompurrrquantregR6rbibutilsRColorBrewerRcppRcppEigenRdpackreformulasrlangrstatixS4ArraysS4VectorsscalesshapeSparseArraySparseMstringistringrSummarizedExperimentsurvivalsurvminersurvMiscsystibbletidyrtidyselecttimechangeUCSC.utilsutf8vctrsviridisLitewithrxfunxml2xtableXVectoryamlzoo

Introduction_1_load_metadata

Hangjia Zhao

Rendered fromIntroduction_1_load_metadata.Rmdusingknitr::rmarkdownon Jan 18 2025.

Last update: 2025-01-17
Started: 2025-01-14

Introduction_2_query_variants

Hangjia Zhao

Rendered fromIntroduction_2_query_variants.Rmdusingknitr::rmarkdownon Jan 18 2025.

Last update: 2025-01-14
Started: 2025-01-14

Introduction_3_access_cnv_frequency

Hangjia Zhao

Rendered fromIntroduction_3_access_cnv_frequency.Rmdusingknitr::rmarkdownon Jan 18 2025.

Last update: 2025-01-14
Started: 2025-01-14

Introduction_4_process_pgxseg

Hangjia Zhao

Rendered fromIntroduction_4_process_pgxseg.Rmdusingknitr::rmarkdownon Jan 18 2025.

Last update: 2025-01-14
Started: 2023-06-14