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Surface Protein Prediction and Identification

Bioconductor version: Release (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>

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


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

if (!require("BiocManager", quietly = TRUE))


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


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

Introduction to SurfR HTML R Script
Reference Manual PDF


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
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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 SurfR_1.0.0.tar.gz
Windows Binary
macOS Binary (x86_64) SurfR_1.0.0.tgz
macOS Binary (arm64) SurfR_1.0.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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Package Short Url
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Old Source Packages for BioC 3.19 Source Archive