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]

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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

4.53 score 15 stars 28 scripts 17 exports 120 dependencies

Last updated 6 months agofrom:895bfd656f. Checks:OK: 1 WARNING: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 16 2024
R-4.5-win-x86_64WARNINGNov 16 2024
R-4.5-linux-x86_64WARNINGNov 16 2024
R-4.4-win-x86_64WARNINGNov 16 2024
R-4.4-mac-x86_64WARNINGNov 16 2024
R-4.4-mac-aarch64WARNINGNov 16 2024
R-4.3-win-x86_64WARNINGNov 16 2024
R-4.3-mac-x86_64WARNINGNov 16 2024
R-4.3-mac-aarch64WARNINGNov 16 2024

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

Dependencies:abindASCATaskpassbackportsBiobaseBiocGenericsBiocManagerbootbroomcarcarDatacliclustercodetoolscolorspacecorrplotcowplotcpp11crayoncurldata.tableDerivdigestDNAcopydoBydoParalleldplyrfansifarverforeachFormulafurrrfuturegenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggplot2ggpubrggrepelggsciggsignifGlobalOptionsglobalsgluegridBasegridExtragtablehttrIRangesisobanditeratorsjsonlitelabelinglatticelgrlifecyclelistenvlme4maftoolsmagrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkmimeminqamltoolsmodelrmunsellnlmenloptrNMFnnetnumDerivopensslparallellypbkrtestpheatmappillarpkgconfigplyrpolynompurrrquadprogquantregR6rappdirsRColorBrewerRcppRcppEigenregistryreshape2RhtslibrjsonrlangrngtoolsrstatixS4VectorsscalessigminerSparseMstringistringrsurvivalsystibbletidyrtidyselectUCSC.utilsutf8uuidvctrsviridisLitewithrxgboostXVectorzlibbioc