Paket: r-bioc-tcgabiolinks (2.30.0+dfsg-1)

[ Kaynak: r-bioc-tcgabiolinks  ]

GNU R/Bioconductor package for integrative analysis with GDC data

The aim of TCGAbiolinks is:

 1) facilitate the GDC open-access data retrieval,
 2) prepare the data using the appropriate pre-processing strategies,
 3) provide the means to carry out different standard analyses and
 4) to easily reproduce earlier research results.

In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.

r-bioc-tcgabiolinks ile İlgili Diğer Paketler

• dep: r-api-4.0

  sanal paketi sağlayan r-base-core

• dep: r-api-bioc-3.18

  sanal paketi sağlayan r-bioc-biocgenerics

• dep: r-bioc-biomart

  GNU R Interface to BioMart databases (Ensembl, COSMIC, Wormbase and Gramene)

• dep: r-bioc-genomicranges

  BioConductor representation and manipulation of genomic intervals

• dep: r-bioc-iranges

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

• dep: r-bioc-s4vectors

  BioConductor S4 implementation of vectors and lists

• dep: r-bioc-summarizedexperiment (>= 1.4.0)

  BioConductor assay container

• dep: r-bioc-tcgabiolinksgui.data (>= 1.15.1)

  Data for the TCGAbiolinksGUI package

• dep: r-cran-data.table

  GNU R extension of Data.frame

• dep: r-cran-downloader (>= 0.4)

  GNU R package for downloading files over http and https

• dep: r-cran-dplyr

  GNU R grammar of data manipulation

• dep: r-cran-ggplot2

  implementation of the Grammar of Graphics

• dep: r-cran-httr (>= 1.2.1)

  GNU R tools for working with URLs and HTTP

• dep: r-cran-jsonlite (>= 1.0.0)

  Robust, High Performance JSON Parser and Generator for R

• dep: r-cran-knitr

  GNU R package for dynamic report generation using Literate Programming

• dep: r-cran-plyr

  tools for splitting, applying and combining data

• dep: r-cran-purrr

  GNU R functional programming tools

• dep: r-cran-r.utils

  GNU R various programming utilities

• dep: r-cran-readr

  GNU R package to read rectangular text data

• dep: r-cran-rvest (>= 0.3.0)

  Easily Harvest (Scrape) Web Pages

• dep: r-cran-stringr (>= 1.0.0)

  Make it easier to work with strings

• dep: r-cran-tibble

  GNU R Simple Data Frames

• dep: r-cran-tidyr

  GNU R package to easily tidy data

• dep: r-cran-xml (>= 3.98.0)

  GNU R package for XML parsing and generation

• dep: r-cran-xml2

  GNU R XML parser

• sug: r-bioc-affy

  BioConductor methods for Affymetrix Oligonucleotide Arrays

• sug: r-bioc-annotationhub

  GNU R client to access AnnotationHub resources

• sug: r-bioc-biobase

  base functions for Bioconductor

• sug: r-bioc-biocstyle

  standard styles for vignettes and other Bioconductor documents

• sug: r-bioc-complexheatmap

  make complex heatmaps using GNU R

• sug: r-bioc-consensusclusterplus

  GNU R determining cluster count and membership

• sug: r-bioc-edaseq

  GNU R exploratory data analysis and normalization for RNA-Seq

• sug: r-bioc-edger

  Empirical analysis of digital gene expression data in R

• sug: r-bioc-experimenthub

  BioConductor client to access ExperimentHub resources

• sug: r-bioc-genefilter

  methods for filtering genes from microarray experiments

• sug: r-bioc-limma

  linear models for microarray data

• sug: r-bioc-sva

  GNU R Surrogate Variable Analysis

• sug: r-cran-circlize

  Circular Visualization

• sug: r-cran-devtools

  Tools to Make Developing R Packages Easier

• sug: r-cran-doparallel

  GNU R foreach parallel adaptor for the parallel package

• sug: r-cran-ggrepel (>= 0.6.3)

  auto-position non-overlapping text labels in plots

• sug: r-cran-gridextra

  GNU R package with extensions for the grid package

• sug: r-cran-igraph

  GNU R network analysis and visualization

• sug: r-cran-jpeg

  Read and write JPEG images

• sug: r-cran-parmigene

  Parallel Mutual Information to establish Gene Networks

• sug: r-cran-png

  GNU R package to read and write PNG images

• sug: r-cran-rmarkdown

  convert R markdown documents into a variety of formats

• sug: r-cran-scales

  Scale functions for visualization

• sug: r-cran-seurat

  Tools for Single Cell Genomics

• sug: r-cran-survival

  GNU R package for survival analysis

• sug: r-cran-survminer

  GNU R drawing survival curves using 'ggplot2'

• sug: r-cran-testthat

  GNU R testsuite

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Mimari	Paket Boyutu	Kurulu Boyut	Dosyalar
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