Package: gcap 1.2.0

gcap: Gene-level Circular Amplicon Prediction

Provides data processing pipeline feeding paired bam files (or allele-specific copy number data) and XGBOOST model for predicting tumor circular amplicons (also known as ecDNA) in gene level.

Authors:Shixiang Wang [aut, cre]

gcap_1.2.0.tar.gz
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gcap.pdf |gcap.html
gcap/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/shixiangwang/gcap/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • ascn - Example allele specific copy number (ASCN) data
  • ec - Example ecDNA training data
  • oncogenes - Oncogene list

On CRAN:

ecdnapipelinetumor-genomicswesxgboost

17 exports 14 stars 2.09 score 129 dependencies

Last updated 1 months agofrom:895bfd656f5d56c3a615e9ad04fb1df63cf37d94

Exports:%>%deployfCNAgcap.ASCNworkflowgcap.collapse2Genesgcap.extractFeaturesgcap.runASCATgcap.runASCNBuildflowgcap.runBuildflowgcap.runPredictiongcap.runScoringgcap.workflowgcap.workflow.facetsgcap.workflow.seqzget_aucmergeDTsoverlaps

Dependencies:abindASCATaskpassbackportsBiobaseBiocGenericsBiocManagerbootbriobroomcallrcarcarDatacliclustercodetoolscolorspacecorrplotcowplotcpp11crayoncurldata.tabledescdiffobjdigestDNAcopydoParalleldplyrevaluatefansifarverforeachfsfurrrfuturegenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggplot2ggpubrggrepelggsciggsignifGlobalOptionsglobalsgluegridBasegridExtragtablehttrIRangesisobanditeratorsjsonlitelabelinglatticelgrlifecyclelistenvlme4maftoolsmagrittrMASSMatrixMatrixModelsmgcvmimeminqamltoolsmunsellnlmenloptrNMFnnetnumDerivopensslparallellypbkrtestpillarpkgbuildpkgconfigpkgloadplyrpolynompraiseprocessxpspurrrquadprogquantregR6rappdirsRColorBrewerRcppRcppEigenregistryrematch2reshape2RhtslibrjsonrlangrngtoolsrprojrootrstatixS4VectorsscalessigminerSparseMstringistringrsurvivalsystestthattibbletidyrtidyselectUCSC.utilsutf8uuidvctrsviridisLitewaldowithrxgboostXVectorzlibbioc