Package: oncoscanR 1.7.0
oncoscanR: Secondary analyses of CNV data (HRD and more)
The software uses the copy number segments from a text file and identifies all chromosome arms that are globally altered and computes various genome-wide scores. The following HRD scores (characteristic of BRCA-mutated cancers) are included: LST, HR-LOH, nLST and gLOH. the package is tailored for the ThermoFisher Oncoscan assay analyzed with their Chromosome Alteration Suite (ChAS) but can be adapted to any input.
Authors:
oncoscanR_1.7.0.tar.gz
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oncoscanR_1.7.0.tgz(r-4.4-any)oncoscanR_1.7.0.tgz(r-4.3-any)
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oncoscanR.pdf |oncoscanR.html✨
oncoscanR/json (API)
NEWS
# Install 'oncoscanR' in R: |
install.packages('oncoscanR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/yannchristinat/oncoscanr/issues
- oncoscan_na33.cov - GenomicRanges object of the chromosomal arms coverage for the oncoscan assay (based on file extdata/Oncoscan.na33.r2.cov.processed.bed).
- segs.chas_example - Expected segments from loading the ChAS file 'chas_example.txt'.
On BioConductor:oncoscanR-1.7.0(bioc 3.20)oncoscanR-1.6.0(bioc 3.19)
Last updated 2 months agofrom:7d61d0528b
Exports:adjust_loharmlevel_altget_amp_segmentsget_gain_segmentsget_hetloss_segmentsget_homloss_segmentsget_loh_segmentsget_loss_segmentsget_oncoscan_coverage_from_bedload_ascatload_chasmerge_segmentsprune_by_sizescore_avgcnscore_estwgdscore_glohscore_lohscore_lstscore_mbaltscore_nlstscore_tdtrim_to_coverageworkflow_oncoscan.ascatworkflow_oncoscan.chas
Dependencies:askpassBiocGenericsbitbit64clicliprcpp11crayoncurlfansiGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehmshttrIRangesjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigprettyunitsprogressR6readrrlangS4VectorssystibbletidyselecttzdbUCSC.utilsutf8vctrsvroomwithrXVectorzlibbioc