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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

Reference Manual PDF

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
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Suggests testthat (>= 3.0.0)
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Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/SurfR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SurfR
Package Short Url https://bioconductor.org/packages/SurfR/
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