r-bioc-purecn (2.12.0+dfsg-2)

Details

Core information at a glance

Distribution
debian
Origin
debian-sid
Repository
https://deb.debian.org/debian
Codename
sid
Component
main
Source
none
Architecture
s390x
Section
gnu-r
Priority
optional
Maintainer
Debian R Packages Maintainers <[email protected]>

Size & integrity

Byte sizes and integrity verification

Installed size
6.9 kB
Size expected
6 MB
Size actual
6 MB
Size match

Dependencies

Required package dependencies

  • r-api-4.0
  • r-api-bioc-3.20
  • r-bioc-dnacopy
  • r-bioc-variantannotation (>= 1.14.1)
  • r-bioc-genomicranges (>= 1.20.3)
  • r-bioc-iranges (>= 2.2.1)
  • r-cran-rcolorbrewer
  • r-bioc-s4vectors
  • r-cran-data.table
  • r-bioc-summarizedexperiment
  • r-bioc-genomeinfodb
  • r-bioc-genomicfeatures
  • r-bioc-rsamtools
  • r-bioc-biobase
  • r-bioc-biostrings
  • r-bioc-biocgenerics
  • r-bioc-rtracklayer
  • r-cran-ggplot2
  • r-cran-gridextra
  • r-cran-futile.logger
  • r-cran-vgam
  • r-cran-mclust
  • r-bioc-rhdf5
  • r-cran-matrix

Suggested packages

Recommended additional packages

  • r-bioc-biocparallel
  • r-bioc-biocstyle
  • r-cran-pscbs
  • r-cran-r.utils
  • r-cran-covr
  • r-cran-knitr
  • r-cran-optparse
  • r-bioc-org.hs.eg.db
  • r-cran-jsonlite
  • r-cran-markdown
  • r-cran-rmarkdown
  • r-cran-testthat

Description

copy number calling and SNV classification using targeted short read sequencing

Homepage Download .deb

Tags

Package classification tags

None

Checksums

Hash values and integrity verification status

TypeActualMatch
MD55d3ae04c…62a48902
SHA-1bb84da14…8333802d
SHA-256bf276129…600845f5
SHA-51258134020…0769d284

Contents

Files and directories included

.
usr
usr/lib
usr/lib/R
usr/lib/R/site-library
usr/lib/R/site-library/PureCN
usr/lib/R/site-library/PureCN/CITATION
usr/lib/R/site-library/PureCN/DESCRIPTION
usr/lib/R/site-library/PureCN/INDEX
usr/lib/R/site-library/PureCN/Meta
usr/lib/R/site-library/PureCN/Meta/Rd.rds
usr/lib/R/site-library/PureCN/Meta/data.rds
usr/lib/R/site-library/PureCN/Meta/features.rds
usr/lib/R/site-library/PureCN/Meta/hsearch.rds
usr/lib/R/site-library/PureCN/Meta/links.rds
usr/lib/R/site-library/PureCN/Meta/nsInfo.rds
usr/lib/R/site-library/PureCN/Meta/package.rds
usr/lib/R/site-library/PureCN/Meta/vignette.rds
usr/lib/R/site-library/PureCN/NAMESPACE
usr/lib/R/site-library/PureCN/NEWS
usr/lib/R/site-library/PureCN/R
usr/lib/R/site-library/PureCN/R/PureCN
usr/lib/R/site-library/PureCN/R/PureCN.rdb
usr/lib/R/site-library/PureCN/R/PureCN.rdx
usr/lib/R/site-library/PureCN/data
usr/lib/R/site-library/PureCN/data/centromeres.rda
usr/lib/R/site-library/PureCN/data/purecn.DNAcopy.bdry.rda
usr/lib/R/site-library/PureCN/data/purecn.example.output.rda
usr/lib/R/site-library/PureCN/doc
usr/lib/R/site-library/PureCN/doc/PureCN.R
usr/lib/R/site-library/PureCN/doc/PureCN.pdf
usr/lib/R/site-library/PureCN/doc/Quick.R
usr/lib/R/site-library/PureCN/doc/index.html
usr/lib/R/site-library/PureCN/extdata
usr/lib/R/site-library/PureCN/extdata/BenchmarkTumorOnly.R
usr/lib/R/site-library/PureCN/extdata/Coverage.R
usr/lib/R/site-library/PureCN/extdata/Dx.R
usr/lib/R/site-library/PureCN/extdata/FilterCallableLoci.R
usr/lib/R/site-library/PureCN/extdata/IntervalFile.R
usr/lib/R/site-library/PureCN/extdata/NormalDB.R
usr/lib/R/site-library/PureCN/extdata/PureCN.R
usr/lib/R/site-library/PureCN/extdata/buggy_cnvkit.seg.gz
usr/lib/R/site-library/PureCN/extdata/dist
usr/lib/R/site-library/PureCN/extdata/dist/calculateSbdry.R
usr/lib/R/site-library/PureCN/extdata/dist/downloadCentromeres.R
usr/lib/R/site-library/PureCN/extdata/ex1.bam
usr/lib/R/site-library/PureCN/extdata/ex1.bam.bai
usr/lib/R/site-library/PureCN/extdata/ex1_gcgene.txt
usr/lib/R/site-library/PureCN/extdata/ex1_intervals.txt
usr/lib/R/site-library/PureCN/extdata/ex1_intervals_headered.txt
usr/lib/R/site-library/PureCN/extdata/ex2_intervals.bed
usr/lib/R/site-library/PureCN/extdata/ex2_intervals.txt
usr/lib/R/site-library/PureCN/extdata/ex2_mappability.bed
usr/lib/R/site-library/PureCN/extdata/ex2_mappability.bigWig
usr/lib/R/site-library/PureCN/extdata/ex2_reference.fa
usr/lib/R/site-library/PureCN/extdata/ex2_reference.fa.fai
usr/lib/R/site-library/PureCN/extdata/ex2_reptiming.bed
usr/lib/R/site-library/PureCN/extdata/ex3_intervals.bed
usr/lib/R/site-library/PureCN/extdata/ex3_mappability.bed
usr/lib/R/site-library/PureCN/extdata/ex3_reference.fa
usr/lib/R/site-library/PureCN/extdata/ex3_reference.fa.fai
usr/lib/R/site-library/PureCN/extdata/example.vcf.gz
usr/lib/R/site-library/PureCN/extdata/example_allelic_counts.tsv
usr/lib/R/site-library/PureCN/extdata/example_callable.bed.gz
usr/lib/R/site-library/PureCN/extdata/example_cosmic.vcf.gz
usr/lib/R/site-library/PureCN/extdata/example_cosmic.vcf.gz.tbi
usr/lib/R/site-library/PureCN/extdata/example_gatk4_denoised_cr.tsv.gz
usr/lib/R/site-library/PureCN/extdata/example_gatk4_modelfinal.seg.gz
usr/lib/R/site-library/PureCN/extdata/example_intervals.txt
usr/lib/R/site-library/PureCN/extdata/example_intervals_tiny.txt
usr/lib/R/site-library/PureCN/extdata/example_intervals_tiny_ot.txt.gz
usr/lib/R/site-library/PureCN/extdata/example_logratio.txt.gz
usr/lib/R/site-library/PureCN/extdata/example_mutect2.vcf.gz
usr/lib/R/site-library/PureCN/extdata/example_mutect2.vcf.gz.tbi
usr/lib/R/site-library/PureCN/extdata/example_normal.list
usr/lib/R/site-library/PureCN/extdata/example_normal.txt.gz
usr/lib/R/site-library/PureCN/extdata/example_normal2.txt.gz
usr/lib/R/site-library/PureCN/extdata/example_normal3.cnn
usr/lib/R/site-library/PureCN/extdata/example_normal4.cnr
usr/lib/R/site-library/PureCN/extdata/example_normal5.hdf5
usr/lib/R/site-library/PureCN/extdata/example_normal_tiny.txt
usr/lib/R/site-library/PureCN/extdata/example_seg.txt
usr/lib/R/site-library/PureCN/extdata/example_single.vcf.gz
usr/lib/R/site-library/PureCN/extdata/example_single.vcf.gz.tbi
usr/lib/R/site-library/PureCN/extdata/example_tumor.txt.gz
usr/lib/R/site-library/PureCN/extdata/example_tumor2.txt.gz
usr/lib/R/site-library/PureCN/extdata/example_tumor_tiny.txt
usr/lib/R/site-library/PureCN/extdata/example_vcf.vcf.gz
usr/lib/R/site-library/PureCN/extdata/example_vcf.vcf.gz.tbi
usr/lib/R/site-library/PureCN/extdata/gatk4_m2_test_pon_db.tgz
usr/lib/R/site-library/PureCN/extdata/gatk4_pon_db.tgz
usr/lib/R/site-library/PureCN/extdata/issue109.vcf.gz
usr/lib/R/site-library/PureCN/extdata/issue184.vcf.gz
usr/lib/R/site-library/PureCN/extdata/issue184_2.vcf.gz
usr/lib/R/site-library/PureCN/extdata/issue184_2_mb.rds
usr/lib/R/site-library/PureCN/extdata/issue192_tumor.cnr
usr/lib/R/site-library/PureCN/extdata/issue192_tumor.seg
usr/lib/R/site-library/PureCN/extdata/issue62.vcf.gz
usr/lib/R/site-library/PureCN/extdata/issue62.vcf.gz.tbi
usr/lib/R/site-library/PureCN/extdata/normalpanel.vcf.gz
usr/lib/R/site-library/PureCN/extdata/normalpanel.vcf.gz.tbi
usr/lib/R/site-library/PureCN/extdata/test_coverage_overlapping_intervals.txt
usr/lib/R/site-library/PureCN/help
usr/lib/R/site-library/PureCN/help/AnIndex
usr/lib/R/site-library/PureCN/help/PureCN.rdb
usr/lib/R/site-library/PureCN/help/PureCN.rdx
usr/lib/R/site-library/PureCN/help/aliases.rds
usr/lib/R/site-library/PureCN/help/paths.rds
usr/lib/R/site-library/PureCN/html
usr/lib/R/site-library/PureCN/html/00Index.html
usr/lib/R/site-library/PureCN/html/R.css
usr/share
usr/share/doc
usr/share/doc/r-bioc-purecn
usr/share/doc/r-bioc-purecn/changelog.Debian.gz
usr/share/doc/r-bioc-purecn/copyright