PureCN specifications

Information


Unique identifier OMICS_14367
Name PureCN
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Already segmented data.
Input format BAM
Output data A histogram of tumor vs. normal copy number log-ratios.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.10.0
Stability Stable
Requirements
stats, RColorBrewer, graphics, BiocGenerics, Rsamtools, DNAcopy, Matrix, utils, testthat, S4Vectors, GenomeInfoDb, Biostrings, rtracklayer, BiocStyle, grDevices, SummarizedExperiment, tools, ggplot2, BiocParallel, GenomicFeatures, R(>=3.3), data.table, knitr, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, VGAM, gridExtra, rhdf5, futile.logger, optparse, VariantAnnotation(>=1.14.1), GenomicRanges(>=1.20.3), IRanges(>=2.2.1), PSCBS
Maintained Yes

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Documentation


Maintainer


  • person_outline Markus Riester <>

Publication for PureCN

PureCN institution(s)
Novartis Institutes for BioMedical Research, Cambridge, MA, USA
PureCN funding source(s)
This work was supported by Novartis Institutes for BioMedical Research.

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