套件：r-bioc-purecn（2.4.0+dfsg-1）

[ 原始碼： 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.

其他與 r-bioc-purecn 有關的套件

• dep: r-api-4.0

  本虛擬套件由這些套件填實： r-base-core

• dep: r-api-bioc-3.16

  本虛擬套件由這些套件填實： r-bioc-biocgenerics

• dep: r-base-core (>= 4.2.2.20221110-1)

  GNU R core of statistical computation and graphics system

• dep: r-bioc-biobase

  base functions for Bioconductor

• 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 extension of Data.frame

• dep: r-cran-futile.logger

  logging utility for GNU R

• dep: r-cran-ggplot2

  implementation of the Grammar of Graphics

• dep: r-cran-gridextra

  GNU R package with extensions for the grid package

• dep: r-cran-matrix

  GNU R package of classes for dense and sparse matrices

• dep: r-cran-mclust

  Gaussian Mixture Modelling for Model-Based Clustering

• dep: r-cran-rcolorbrewer

  GNU R package providing suitable color palettes

• dep: r-cran-vgam

  GNU R package for estimating vector generalized additive models

• 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-markdown

  GNU R package providing R bindings to the Sundown Markdown rendering library

• 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-r.utils

  GNU R various programming utilities

• sug: r-cran-rmarkdown

  convert R markdown documents into a variety of formats

• sug: r-cran-testthat

  GNU R testsuite

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