Balík: r-bioc-purecn (2.10.0+dfsg-1)

[ Zdroj: 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.

Ostatné balíky súvisiace s balíkom r-bioc-purecn

• dep: r-api-4.0

  virtuálny balík poskytovaný balíkom r-base-core

• dep: r-api-bioc-3.19

  virtuálny balík poskytovaný balíkom r-bioc-biocgenerics

• dep: r-bioc-biobase (>= 2.64.0)

  base functions for Bioconductor

• dep: r-bioc-biocgenerics (>= 0.50.0)

  generic functions for Bioconductor

• dep: r-bioc-biostrings (>= 2.72.1)

  GNU R string objects representing biological sequences

• dep: r-bioc-dnacopy (>= 1.78.0)

  R package: DNA copy number data analysis

• dep: r-bioc-genomeinfodb (>= 1.40.1)

  BioConductor utilities for manipulating chromosome identifiers

• dep: r-bioc-genomicfeatures (>= 1.56.0)

  GNU R tools for making and manipulating transcript centric annotations

• dep: r-bioc-genomicranges (>= 1.56.1)

  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 (>= 2.48.0)

  BioConductor HDF5 interface to R

• dep: r-bioc-rsamtools (>= 2.20.0)

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

• dep: r-bioc-rtracklayer (>= 1.64.0)

  GNU R interface to genome browsers and their annotation tracks

• dep: r-bioc-s4vectors (>= 0.42.1)

  BioConductor S4 implementation of vectors and lists

• dep: r-bioc-summarizedexperiment (>= 1.34.0)

  BioConductor assay container

• dep: r-bioc-variantannotation (>= 1.50.0)

  BioConductor annotation of genetic variants

• dep: r-cran-data.table

  GNU R - rozšírenie Data.frame

• dep: r-cran-futile.logger

  logging utility for GNU R

• dep: r-cran-ggplot2

  implementácia Gramatiky grafiky

• dep: r-cran-gridextra

  GNU R - balík s rozšíreniami balíka grid

• dep: r-cran-matrix

  balík tried GNU R pre husté a riedke matice

• dep: r-cran-mclust

  Gaussian Mixture Modelling for Model-Based Clustering

• dep: r-cran-rcolorbrewer

  balík GNU R poskytujúci vhodné palety farieb

• 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

  robustný, výkonný nástroj na tvorbu a spracovanie JSON pre R

• sug: r-cran-knitr

  balík GNU R na dynamickú tvorbu zostáv pomocou Literate Programming

• sug: r-cran-markdown

  balík GNU R poskytujúci väzby knižnice Sundown na vykresľovanie Markdown pre jazyk R

• 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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