Package: CODEX 1.39.0
Yuchao Jiang
CODEX: A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing
A normalization and copy number variation calling procedure for whole exome DNA sequencing data. CODEX relies on the availability of multiple samples processed using the same sequencing pipeline for normalization, and does not require matched controls. The normalization model in CODEX includes terms that specifically remove biases due to GC content, exon length and targeting and amplification efficiency, and latent systemic artifacts. CODEX also includes a Poisson likelihood-based recursive segmentation procedure that explicitly models the count-based exome sequencing data.
Authors:
CODEX_1.39.0.tar.gz
CODEX_1.39.0.zip(r-4.5)CODEX_1.39.0.zip(r-4.4)CODEX_1.39.0.zip(r-4.3)
CODEX_1.39.0.tgz(r-4.5-any)CODEX_1.39.0.tgz(r-4.4-any)CODEX_1.39.0.tgz(r-4.3-any)
CODEX_1.39.0.tar.gz(r-4.5-noble)CODEX_1.39.0.tar.gz(r-4.4-noble)
CODEX_1.39.0.tgz(r-4.4-emscripten)CODEX_1.39.0.tgz(r-4.3-emscripten)
CODEX.pdf |CODEX.html✨
CODEX/json (API)
NEWS
| # Install 'CODEX' in R: |
| install.packages('CODEX', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- bambedObjDemo - Demo data pre-stored for bambedObj.
- coverageObjDemo - Demo data pre-stored for coverageObj.
- gcDemo - Demo data pre-stored for GC content.
- mappDemo - Demo data pre-stored for mappability.
- mapp_ref - Position reference for pre-computed mappability results.
- mappability - Pre-computed mappabilities
- normObjDemo - Demo data pre-stored for normObj.
- qcObjDemo - Demo data pre-stored for qcObj.
On BioConductor:CODEX-1.39.0(bioc 3.21)CODEX-1.38.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologyexomeseqnormalizationqualitycontrolcopynumbervariation
Last updated 5 months agofrom:a803161f17. Checks:1 OK, 8 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 29 2025 |
| R-4.5-win | NOTE | Mar 29 2025 |
| R-4.5-mac | NOTE | Mar 29 2025 |
| R-4.5-linux | NOTE | Mar 29 2025 |
| R-4.4-win | NOTE | Mar 29 2025 |
| R-4.4-mac | NOTE | Mar 29 2025 |
| R-4.4-linux | NOTE | Mar 29 2025 |
| R-4.3-win | NOTE | Mar 29 2025 |
| R-4.3-mac | NOTE | Mar 29 2025 |
Exports:choiceofKgetbambedgetcoveragegetgcgetmappnormalizenormalize2qcsegment
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomeBSgenome.Hsapiens.UCSC.hg19codetoolscpp11crayoncurlDelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangeshttrIRangesjsonlitelambda.rlatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6RCurlrestfulrRhtslibrjsonRsamtoolsrtracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsXMLXVectoryaml
