Package: cfDNAPro 1.19.0

Haichao Wang

cfDNAPro: cfDNAPro extracts and Visualises biological features from whole genome sequencing data of cell-free DNA

cfDNA fragments carry important features for building cancer sample classification ML models, such as fragment size, and fragment end motif etc. Analyzing and visualizing fragment size metrics, as well as other biological features in a curated, standardized, scalable, well-documented, and reproducible way might be time intensive. This package intends to resolve these problems and simplify the process. It offers two sets of functions for cfDNA feature characterization and visualization.

Authors:Haichao Wang [aut, cre], Hui Zhao [ctb], Elkie Chan [ctb], Christopher Smith [ctb], Tomer Kaplan [ctb], Florian Markowetz [ctb], Nitzan Rosenfeld [ctb]

cfDNAPro_1.19.0.tar.gz
cfDNAPro_1.19.0.zip(r-4.7)cfDNAPro_1.19.0.zip(r-4.6)cfDNAPro_1.19.0.zip(r-4.5)
cfDNAPro_1.19.0.tgz(r-4.6-any)cfDNAPro_1.19.0.tgz(r-4.5-any)
cfDNAPro_1.19.0.tar.gz(r-4.7-any)cfDNAPro_1.19.0.tar.gz(r-4.6-any)
cfDNAPro_1.19.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cfDNAPro/json (API)

# Install 'cfDNAPro' in R:

install.packages('cfDNAPro', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/hw538/cfdnapro/issues

On BioConductor:cfDNAPro-1.19.0(bioc 3.24)cfDNAPro-1.18.0(bioc 3.23)

visualization sequencing wholegenome bioinformatics cancer-genomics cancer-research cell-free-dna early-detection genomics-visualization liquid-biopsy swgs whole-genome-sequencing

6.59 score 43 stars 15 scripts 15 exports 84 dependencies

Last updated from:2229399743. Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	346
linux-devel-x86_64	WARNING	450
source / vignettes	OK	461
linux-release-x86_64	WARNING	467
macos-release-arm64	WARNING	304
macos-oldrel-arm64	WARNING	297
windows-devel	WARNING	346
windows-release	WARNING	346
windows-oldrel	WARNING	333
wasm-release	OK	317

Exports:callMetrics callMode callPeakDistance callSize callValleyDistance examplePath plotAllToOne plotMetrics plotMode plotModeSummary plotPeakDistance plotSingleGroup plotValleyDistance read_bam_insert_metrics readBam

Dependencies:abind askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bitops BSgenome BSgenome.Hsapiens.NCBI.GRCh38 BSgenome.Hsapiens.UCSC.hg19 BSgenome.Hsapiens.UCSC.hg38 cigarillo cli codetools cpp11 crayon curl DelayedArray dplyr farver formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite labeling lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats mime openssl pillar pkgconfig plyranges quantmod R6 RColorBrewer RCurl restfulr Rhtslib rjson rlang Rsamtools rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyselect TTR UCSC.utils utf8 vctrs viridisLite withr XML xts XVector yaml zoo

cfDNAPro

Rendered fromcfDNAPro.Rmdusingknitr::rmarkdown

Last update: 2021-07-19
Started: 2021-05-26

Help page	Topics
Calculate the metrics of insert size	callMetrics
Calculate the mode fragment size of each sample	callMode
Calculate the inter-peak distance of insert size	callPeakDistance
Calculate the insert size metrics (i.e. prop, cdf, 1-cdf) or each group	callSize
Calculate the inter-valley distance of insert size	callValleyDistance
Get path to cfDNAPro example folder.	examplePath
Plot the raw fragment size metrics (e.g. proportion, cdf and 1-cdf) of all groups with different colors in a single plot	plotAllToOne
Plot the fragment size metrics (i.e. proportion, cdf and 1-cdf)	plotMetrics
Plot mode fragment size	plotMode
Summarize and plot mode fragment size in a stacked bar chart	plotModeSummary
Plot the inter-peak distance of fragment size distance distribution	plotPeakDistance
Plot the raw fragment size metrics of single group in a single plot, colored by samples.	plotSingleGroup
Plot the inter-valley distance of fragment size distance distribution	plotValleyDistance
Calculate insert sizes from a curated GRanges object	read_bam_insert_metrics
Read bam file into a curated GRanges object	readBam

Package: cfDNAPro 1.19.0

cfDNAPro: cfDNAPro extracts and Visualises biological features from whole genome sequencing data of cell-free DNA

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Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)