SurfR

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see SurfR.

Surface Protein Prediction and Identification

Bioconductor version: 3.19

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] , Anna Sofia Tascini [aut, ctb]

Maintainer: Aurora Maurizio <auroramaurizio1 at gmail.com>

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

Installation

To install this package, start R (version "4.4") 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")

Introduction to SurfR HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews BatchEffect, DataImport, DifferentialExpression, FunctionalGenomics, FunctionalPrediction, GO, GeneExpression, GenePrediction, GeneSetEnrichment, Pathways, PrincipalComponent, RNASeq, Sequencing, Software, Transcription, Visualization

Version 1.0.0

In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)

License GPL-3 + file LICENSE

Depends R (>= 4.3.0)

Imports httr, BiocFileCache, BiocStyle, SPsimSeq, DESeq2, edgeR, openxlsx, stringr, rhdf5, ggplot2, ggrepel, stats, magrittr, assertr, tidyr, dplyr, TCGAbiolinks, biomaRt, metaRNASeq, enrichR, scales, venn, gridExtra, SummarizedExperiment, knitr, grDevices, graphics, utils

System Requirements

URL https://github.com/auroramaurizio/SurfR

Bug Reports https://github.com/auroramaurizio/SurfR/issues

Suggests testthat (>= 3.0.0)

Linking To

Enhances

Depends On Me

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Build Report Build Report

Package Archives

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

Source Package SurfR_1.0.0.tar.gz

Windows Binary (x86_64) SurfR_1.0.0.zip

macOS Binary (x86_64) SurfR_1.0.0.tgz

macOS Binary (arm64) SurfR_1.0.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/SurfR

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SurfR

Bioc Package Browser https://code.bioconductor.org/browse/SurfR/

Package Short Url https://bioconductor.org/packages/SurfR/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.19 Source Archive