Package: cfdnakit 1.5.0

Pitithat Puranachot

cfdnakit: Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA)

This package provides basic functions for analyzing shallow whole-genome sequencing (~0.3X or more) of cell-free DNA (cfDNA). The package basically extracts the length of cfDNA fragments and aids the vistualization of fragment-length information. The package also extract fragment-length information per non-overlapping fixed-sized bins and used it for calculating ctDNA estimation score (CES).

Authors:Pitithat Puranachot [aut, cre]

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cfdnakit.pdf |cfdnakit.html✨
cfdnakit/json (API)
NEWS

# Install 'cfdnakit' in R:
install.packages('cfdnakit', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/pitithat-pu/cfdnakit/issues

On BioConductor:cfdnakit-1.5.0(bioc 3.21)cfdnakit-1.4.0(bioc 3.20)

copynumbervariationsequencingwholegenome

5.24 score 7 stars 8 scripts 114 downloads 15 exports 84 dependencies

Last updated 23 days agofrom:889853b551. Checks:OK: 3 WARNING: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 09 2024
R-4.5-winWARNINGNov 09 2024
R-4.5-linuxWARNINGNov 09 2024
R-4.4-winWARNINGNov 09 2024
R-4.4-macOKNov 09 2024
R-4.3-winWARNINGNov 09 2024
R-4.3-macOKNov 09 2024

Exports:calculate_CES_scorecall_cnvcreate_PoNextract_insert_sizeget_fragment_profileget_solution_tableget_zscore_profileplot_cnv_solutionplot_distance_matrixplot_fragment_distplot_sl_ratioplot_transformed_slread_bamfilesegmentByPSCBtest_isize_KolmogorovSmirnov

Dependencies:aroma.lightaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitopsCGHbaseCGHcallclicodetoolscolorspacecpp11crayoncurldigestDNAcopydplyrfansifarverformatRfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2globalsgluegtablehttrimputeIRangesisobandjsonlitelabelinglambda.rlatticelifecyclelimmalistenvmagrittrmarrayMASSMatrixmatrixStatsmgcvmimemunsellnlmeopensslparallellypillarpkgconfigPSCBSQDNAseqR.cacheR.methodsS3R.ooR.utilsR6RColorBrewerRhtslibrlangRsamtoolsS4VectorsscalessnowsnowfallstatmodsystibbletidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

cfdnakit vignette

Pitithat Puranachot

Rendered fromcfdnakit-vignette.Rmdusingknitr::rmarkdownon Nov 09 2024.

Last update: 2023-05-27
Started: 2022-11-09

Readme and manuals

Help Manual

Help pageTopics
Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA)cfdnakit-package cfdnakit
Calculate CES Score from Segmentationcalculate_CES_score
Call Copy-number Variation from SLRatio and segmentationcall_cnv
Create Blacklist regions GRanges objectcreate_blacklist_gr
Create Panel-of-Normal (PoN) objectcreate_PoN
Extract Insert size from SampleBamextract_insert_size
Filter out reads on blacklist regionsfilter_read_on_blacklist
Get insert-size distribution tablefragment_dist
Getting fragment-length informationget_fragment_profile
Return CNV segmentation result from given all CNV solutionsget_segment_bysolution
Get summarised table of cnv solutionsget_solution_table
Transform SLRatio with PoN Fragment profileget_zscore_profile
Convert GRCh chromosome format to UCSC styleGRCh2UCSCGRanges
Check if bai file exist from given bamif_exist_baifile
Check UCSC chromosomes format for input bam fileif_ucsc_chrformat
Make Fragment-length density tablemake_density_table
Overlap and merge bin data frame with segmentation dataframeoverlap_bin_with_segment
Plot Fragment-length profile with CNV calling resultplot_cnv_solution
Plot Distance Matrix from CNVCallingplot_distance_matrix
Plot Fragment-length Distributionplot_fragment_dist
Plot Short/Long-fragment Ratioplot_sl_ratio
Plot z-tranformed Short/Long-fragment Ratioplot_transformed_sl
Read a bam file Read a bam file from give path. Alignment and sequencing read information will be binned into non-overlapping sizeread_bamfile
Read Fragment Profile from a list of rds fileread_PoN_files
Segmentation data with PSCBSsegmentByPSCB
KolmogorovSmirnov test for insert sizetest_isize_KolmogorovSmirnov
Convert UCSC chromosome format to GRCh style from a list of alignment informationUCSC2GRChSampleBam
Correct GC Bias readcountutil.bias_correct
zscore_transform transforms SLRatio profile into z-scorezscore_transform