ctDNAtools: Analyze Circulating Tumor DNA Sequencing Data

Contains tools to analyze minimal residual disease and cell-free DNA fragmentation from aligned sequencing data. More details on the methods can be found in: Amjad Alkodsi, Leo Meriranta, Annika Pasanen, Sirpa Leppä (2020) <doi:10.1101/2020.01.27.912790>.

Version: 0.4.0
Depends: R (≥ 3.6.0)
Imports: magrittr, dplyr (≥ 0.8.3), tidyr (≥ 1.0.0), purrr (≥ 0.3.2), Rsamtools (≥ 2.0.0), assertthat (≥ 0.2.1), GenomicRanges, IRanges, GenomeInfoDb, BiocGenerics, BSgenome, GenomicAlignments, rlang (≥ 0.4.0), Biostrings, methods, furrr (≥ 0.1.0), ellipsis (≥ 0.3.0), VariantAnnotation (≥ 1.30.1)
Suggests: BSgenome.Hsapiens.UCSC.hg19, testthat (≥ 2.1.0), ggplot2, knitr, rmarkdown, covr, pkgdown
Published: 2020-03-04
Author: Amjad Alkodsi ORCID iD [aut, cre]
Maintainer: Amjad Alkodsi <amjad.alkodsi at gmail.com>
BugReports: https://github.com/alkodsi/ctDNAtools/issues
License: MIT + file LICENSE
URL: https://github.com/alkodsi/ctDNAtools
NeedsCompilation: no
Citation: ctDNAtools citation info
Materials: README
CRAN checks: ctDNAtools results


Reference manual: ctDNAtools.pdf
Vignettes: Analysis of ctDNA sequencing data with ctDNAtools
Package source: ctDNAtools_0.4.0.tar.gz
Windows binaries: r-devel: ctDNAtools_0.4.0.zip, r-release: ctDNAtools_0.4.0.zip, r-oldrel: ctDNAtools_0.4.0.zip
macOS binaries: r-release: ctDNAtools_0.4.0.tgz, r-oldrel: not available


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