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'))

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:

ecdna pipeline tumor-genomics wes xgboost

17 exports 14 stars 2.00 score 118 dependencies

Last updated 2 months agofrom:895bfd656f

Exports:%>%deploy fCNA gcap.ASCNworkflow gcap.collapse2Genes gcap.extractFeatures gcap.runASCAT gcap.runASCNBuildflow gcap.runBuildflow gcap.runPrediction gcap.runScoring gcap.workflow gcap.workflow.facets gcap.workflow.seqz get_auc mergeDTs overlaps

Dependencies:abind ASCAT askpass backports Biobase BiocGenerics BiocManager boot broom car carData cli cluster codetools colorspace corrplot cowplot cpp11 crayon curl data.table Deriv digest DNAcopy doBy doParallel dplyr fansi farver foreach furrr future generics GenomeInfoDb GenomeInfoDbData GenomicRanges GetoptLong ggplot2 ggpubr ggrepel ggsci ggsignif GlobalOptions globals glue gridBase gridExtra gtable httr IRanges isoband iterators jsonlite labeling lattice lgr lifecycle listenv lme4 maftools magrittr MASS Matrix MatrixModels mgcv microbenchmark mime minqa mltools modelr munsell nlme nloptr NMF nnet numDeriv openssl parallelly pbkrtest pillar pkgconfig plyr polynom purrr quadprog quantreg R6 rappdirs RColorBrewer Rcpp RcppEigen registry reshape2 Rhtslib rjson rlang rngtools rstatix S4Vectors scales sigminer SparseM stringi stringr survival sys tibble tidyr tidyselect UCSC.utils utf8 uuid vctrs viridisLite withr xgboost XVector zlibbioc

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Example allele specific copy number (ASCN) data	ascn
Deploy Command Line Interface to System Local Path	deploy
Example ecDNA training data	ec
R6 class representing focal copy number amplification list predicted from a cohort	fCNA
GCAP workflow for gene-level amplicon prediction from ASCN input	gcap.ASCNworkflow
Generate unified gene-level feature data	gcap.collapse2Genes
Extract sample and region level features	gcap.extractFeatures
Run ASCAT on tumor-normal pair WES data files	gcap.runASCAT
Build data for prediction from absolute copy number data	gcap.runASCNBuildflow
Build data for prediction from ASCAT result files	gcap.runBuildflow
Run gene-level circular prediction	gcap.runPrediction
Summarize prediction result into gene/sample-level	gcap.runScoring
GCAP workflow for gene-level amplicon prediction	gcap.workflow
GCAP FACETS workflow for gene-level amplicon prediction	gcap.workflow.facets
GCAP sequenza workflow for gene-level amplicon prediction	gcap.workflow.seqz
Get AUC value	get_auc
Merge a list of data.table	mergeDTs
Oncogene list	oncogenes
Get overlaps of two genomic regions	overlaps