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:
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')) |
Bug tracker:https://github.com/shixiangwang/gcap/issues
Pkgdown:https://shixiangwang.github.io
ecdnapipelinetumor-genomicswesxgboost
Last updated 7 months agofrom:895bfd656f. Checks:OK: 1 WARNING: 8. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 16 2024 |
R-4.5-win-x86_64 | WARNING | Nov 16 2024 |
R-4.5-linux-x86_64 | WARNING | Nov 16 2024 |
R-4.4-win-x86_64 | WARNING | Nov 16 2024 |
R-4.4-mac-x86_64 | WARNING | Nov 16 2024 |
R-4.4-mac-aarch64 | WARNING | Nov 16 2024 |
R-4.3-win-x86_64 | WARNING | Nov 16 2024 |
R-4.3-mac-x86_64 | WARNING | Nov 16 2024 |
R-4.3-mac-aarch64 | WARNING | Nov 16 2024 |
Exports:%>%deployfCNAgcap.ASCNworkflowgcap.collapse2Genesgcap.extractFeaturesgcap.runASCATgcap.runASCNBuildflowgcap.runBuildflowgcap.runPredictiongcap.runScoringgcap.workflowgcap.workflow.facetsgcap.workflow.seqzget_aucmergeDTsoverlaps
Dependencies:abindASCATaskpassbackportsBiobaseBiocGenericsBiocManagerbootbroomcarcarDatacliclustercodetoolscolorspacecorrplotcowplotcpp11crayoncurldata.tableDerivdigestDNAcopydoBydoParalleldplyrfansifarverforeachFormulafurrrfuturegenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggplot2ggpubrggrepelggsciggsignifGlobalOptionsglobalsgluegridBasegridExtragtablehttrIRangesisobanditeratorsjsonlitelabelinglatticelgrlifecyclelistenvlme4maftoolsmagrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkmimeminqamltoolsmodelrmunsellnlmenloptrNMFnnetnumDerivopensslparallellypbkrtestpheatmappillarpkgconfigplyrpolynompurrrquadprogquantregR6rappdirsRColorBrewerRcppRcppEigenregistryreshape2RhtslibrjsonrlangrngtoolsrstatixS4VectorsscalessigminerSparseMstringistringrsurvivalsystibbletidyrtidyselectUCSC.utilsutf8uuidvctrsviridisLitewithrxgboostXVectorzlibbioc