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SurfR

This is the development version of SurfR; to use it, please install the devel version of Bioconductor.

Surface Protein Prediction and Identification


Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews BatchEffect, DataImport, DifferentialExpression, FunctionalGenomics, FunctionalPrediction, GO, GeneExpression, GenePrediction, GeneSetEnrichment, Pathways, PrincipalComponent, RNASeq, Sequencing, Software, Transcription, Visualization
Version 0.99.54
In Bioconductor since BioC 3.19 (R-4.4)
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
See More
Suggests testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports 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_0.99.54.tar.gz
Windows Binary SurfR_0.99.54.zip
macOS Binary (x86_64) SurfR_0.99.54.tgz
macOS Binary (arm64) SurfR_0.99.54.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