seqCNA: Copy number analysis of high-throughput sequencing cancer data

Share:

Copy number analysis of high-throughput sequencing cancer data with fast summarization, extensive filtering and improved normalization

Author
David Mosen-Ansorena
Date of publication
None
Maintainer
David Mosen-Ansorena <dmosen.gn@cicbiogune.es>
License
GPL-3
Version
1.20.0

View on Bioconductor

Man pages

applyFilters
The function applies a set of filters to the raw profile.
applyThresholds
Apply thresholds on the segmented profile in order to call...
plotCNProfile
Plots the profile of a 'SeqCNAInfo-class' object.
readSeqsumm
Function that reads seqsumm summarized files.
runGLAD
Wrapper function that runs the GLAD segmentation algorithm on...
runSeqnorm
This function calls seqnorm, which normalizes the tumoural...
runSeqsumm
Function that generates seqsumm summarized files.
SeqCNAInfo-class
Class '"SeqCNAInfo"'
seqCNA-package
Copy number analysis of deep sequencing cancer data
seqsumm_HCC1143
Example of a seqsumm output, namely for a sequenced sample of...
writeCNProfile
Outputs the processed profile of a 'SeqCNAInfo-class' object...

Files in this package

seqCNA/DESCRIPTION
seqCNA/NAMESPACE
seqCNA/R
seqCNA/R/AllClasses.R
seqCNA/R/AllGenerics.R
seqCNA/R/overLapper.R
seqCNA/R/seqCNA-internal.R
seqCNA/R/seqCNA_functions.r
seqCNA/R/summary-methods.R
seqCNA/build
seqCNA/build/vignette.rds
seqCNA/data
seqCNA/data/seqsumm_HCC1143.txt.gz
seqCNA/inst
seqCNA/inst/CITATION
seqCNA/inst/doc
seqCNA/inst/doc/seqCNA.R
seqCNA/inst/doc/seqCNA.Rnw
seqCNA/inst/doc/seqCNA.pdf
seqCNA/inst/extdata
seqCNA/inst/extdata/test.sam
seqCNA/man
seqCNA/man/SeqCNAInfo-class.Rd
seqCNA/man/applyFilters.Rd
seqCNA/man/applyThresholds.Rd
seqCNA/man/plotCNProfile.Rd
seqCNA/man/readSeqsumm.Rd
seqCNA/man/runGLAD.Rd
seqCNA/man/runSeqnorm.Rd
seqCNA/man/runSeqsumm.Rd
seqCNA/man/seqCNA-package.Rd
seqCNA/man/seqsumm_HCC1143.Rd
seqCNA/man/writeCNProfile.Rd
seqCNA/src
seqCNA/src/seqCNA.cpp
seqCNA/vignettes
seqCNA/vignettes/seqCNA.Rnw
seqCNA/vignettes/seqCNA.bib