Paket: r-bioc-purecn (1.20.0+dfsg-3)

[ Quellcode: r-bioc-purecn  ]

copy number calling and SNV classification using targeted short read sequencing

This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number pipelines, and has support for tumor samples without matching normal samples.

Andere Pakete mit Bezug zu r-bioc-purecn

• dep: r-api-4.0

  virtuelles Paket, bereitgestellt durch r-base-core

• dep: r-api-bioc-3.12

  virtuelles Paket, bereitgestellt durch r-bioc-biocgenerics

• dep: r-base-core (>= 4.0.3-1)

  GNU R - System für statistische Berechnungen und Grafik - Kern

• dep: r-bioc-biocgenerics

  generic functions for Bioconductor

• dep: r-bioc-biostrings

  GNU R string objects representing biological sequences

• dep: r-bioc-dnacopy

  R package: DNA copy number data analysis

• dep: r-bioc-genomeinfodb

  BioConductor utilities for manipulating chromosome identifiers

• dep: r-bioc-genomicfeatures

  GNU R tools for making and manipulating transcript centric annotations

• dep: r-bioc-genomicranges (>= 1.20.3)

  BioConductor representation and manipulation of genomic intervals

• dep: r-bioc-iranges (>= 2.2.1)

  GNU R low-level containers for storing sets of integer ranges

• dep: r-bioc-rhdf5

  BioConductor HDF5 interface to R

• dep: r-bioc-rsamtools

  GNU R binary alignment (BAM), variant call (BCF), or tabix file import

• dep: r-bioc-rtracklayer

  GNU R interface to genome browsers and their annotation tracks

• dep: r-bioc-s4vectors

  BioConductor S4 implementation of vectors and lists

• dep: r-bioc-summarizedexperiment

  BioConductor assay container

• dep: r-bioc-variantannotation (>= 1.14.1)

  BioConductor annotation of genetic variants

• dep: r-cran-data.table

  GNU R - Erweiterung von data.frame()

• dep: r-cran-futile.logger

  logging utility for GNU R

• dep: r-cran-ggplot2

  Implementierung der »Grammar of Graphics«

• dep: r-cran-gridextra

  GNU R: Erweiterungen für das grid-Paket

• dep: r-cran-matrix

  GNU R - Paket von Klassen für dicht und dünn besetzte Matrizen

• dep: r-cran-rcolorbrewer

  GNU R package providing suitable color palettes

• dep: r-cran-vgam

  GNU R package for estimating vector generalized additive models

• rec: r-cran-testthat

  GNU R testsuite

• sug: r-bioc-biocparallel

  BioConductor facilities for parallel evaluation

• sug: r-bioc-biocstyle

  standard styles for vignettes and other Bioconductor documents

• sug: r-bioc-org.hs.eg.db

  genome-wide annotation for Human

• sug: r-cran-covr

  test coverage for GNU R packages

• sug: r-cran-jsonlite

  Robust, High Performance JSON Parser and Generator for R

• sug: r-cran-knitr

  GNU R package for dynamic report generation using Literate Programming

• sug: r-cran-optparse

  GNU/R Command line option parser

• sug: r-cran-pscbs

  R package: Analysis of Parent-Specific DNA Copy Numbers

• sug: r-cran-rmarkdown

  Konvertierung von R-Markdown-Dokumenten in verschiedene Formate

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Architektur	Paketgröße	Größe (installiert)	Dateien
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