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_1.2.0.tgz(r-4.5-emscripten)
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'))

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

Pkgdown/docs site:https://shixiangwang.github.io

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:

Conda:

ecdnapipelinetumor-genomicswesxgboostcpp

3.91 score 20 stars 41 scripts 17 exports 124 dependencies

Last updated from:c36c65b827. Checks:11 ERROR, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64ERROR228
linux-devel-x86_64ERROR265
source / vignettesOK239
linux-release-arm64ERROR241
linux-release-x86_64ERROR275
macos-devel-arm64ERROR282
macos-devel-x86_64ERROR462
macos-release-arm64ERROR169
macos-release-x86_64ERROR304
windows-develERROR216
windows-releaseERROR230
windows-oldrelERROR268
wasm-releaseOK185

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

Dependencies:abindASCATbackportsBiobaseBiocGenericsBiocManagerbootbroomcarcarDatacliclustercodetoolscolorspacecorrplotcowplotcpp11crayoncurldata.tableDerivdigestDNAcopydoBydoParalleldplyrfarverforeachforecastFormulafracdifffurrrfuturegenericsGenomicRangesGetoptLongggplot2ggpubrggrepelggsciggsignifGlobalOptionsglobalsgluegridBasegridExtragtableIRangesisobanditeratorsjsonlitelabelinglatticelgrlifecyclelistenvlme4lmtestmaftoolsmagrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkminqamltoolsmodelrnlmenloptrNMFnnetnumDerivparallellypbkrtestpheatmappillarpkgconfigplyrpolynompurrrquadprogquantmodquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasregistryreshape2RhtslibrjsonrlangrngtoolsrstatixS4VectorsS7scalesSeqinfosigminerSparseMstringistringrsurvivaltibbletidyrtidyselecttimeDatetseriesTTRurcautf8uuidvctrsviridisLitewithrxgboostxtszoo