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Bioconductor - SurfR

SurfR

This is the released version of SurfR; for the devel version, see SurfR.

Surface Protein Prediction and Identification

Bioconductor version: Release (3.21)

Identify Surface Protein coding genes from a list of candidates. Systematically download data from GEO and TCGA or use your own data. Perform DGE on bulk RNAseq data. Perform Meta-analysis. Descriptive enrichment analysis and plots.

Author: Aurora Maurizio [aut, cre] ORCID: 0000-0002-7194-4637 , Anna Sofia Tascini [aut, ctb] ORCID: 0000-0001-5731-5490

Maintainer: Aurora Maurizio <auroramaurizio1 at gmail.com>

Citation (from within R, enter citation("SurfR")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SurfR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SurfR")
Details biocViews BatchEffect, DataImport, DifferentialExpression, FunctionalGenomics, FunctionalPrediction, GO, GeneExpression, GenePrediction, GeneSetEnrichment, Pathways, PrincipalComponent, RNASeq, Sequencing, Software, Transcription, Visualization Version 1.4.1 In Bioconductor since BioC 3.19 (R-4.4) (1 year) License GPL-3 + file LICENSE Depends R (>= 4.4.0) Imports httr, BiocFileCache, SPsimSeq, DESeq2, edgeR, openxlsx, stringr, rhdf5, ggplot2, ggrepel, stats, magrittr, assertr, tidyr, dplyr, TCGAbiolinks, biomaRt, metaRNASeq, scales, venn, gridExtra, SummarizedExperiment, knitr, rjson, grDevices, graphics, curl, utils System Requirements URL https://github.com/auroramaurizio/SurfR Bug Reports https://github.com/auroramaurizio/SurfR/issues See More Package Archives

Follow Installation instructions to use this package in your R session.

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