In marziasettino/MMRFBiolinks: R package for integrative analysis of MMRF-CoMMpass data

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(MMRFBiolinks)

MMRFBiolinks leverages TCGAbiolinks package for searching, downloading and preparing data from the Multiple Myeloma Research Foundation (MMRF) CoMMpass study available at the NCI's Genomic Data Commons (GDC) Data Portal.

Citation

If you use MMRFBiolinks, please cite:

• Settino M, Cannataro M. MMRFBiolinks: an R-package for integrating and analyzing MMRF-CoMMpass data

• Colaprico A, Silva TC, Olsen C, Garofano L, Cava C, Garolini D, Sabedot T, Malta TM, Pagnotta SM, Castiglioni I, Ceccarelli M, Bontempi G and Noushmehr H. "TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data." Nucleic acids research (2015): gkv1507.

• Mounir, Mohamed, Lucchetta, Marta, Silva, C T, Olsen, Catharina, Bontempi, Gianluca, Chen, Xi, Noushmehr, Houtan, Colaprico, Antonio, Papaleo, Elena (2019). “New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx.” PLoS computational biology, 15(3), e1006701.

• Silva TC, Colaprico A, Olsen C et al.TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages [version 2; peer review: 1 approved, 2 approved with reservations]. F1000Research 2016, 5:1542 (https://doi.org/10.12688/f1000research.8923.2)

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Download and Install

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To install this package, start R (version "4.0.0") and enter:

devtools::install_github("marziasettino/MMRFBiolinks", build_vignettes = TRUE)
library(MMRFBiolinks)

Question and issues

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Please use Github issues if you want to file bug reports or feature requests

Required libraries

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The examples in this tutorial use the following libraries:

library(TCGAbiolinks)
library(SummarizedExperiment)
library(dplyr)
library(DT)
library(ggplot2)

Session info

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version
packageVersion("MMRFBiolinks")

marziasettino/MMRFBiolinks documentation built on Jan. 24, 2023, 4:49 a.m.