SurfR
This is the released version of SurfR; for the devel version, see SurfR.
Surface Protein Prediction and Identification
Bioconductor version: Release (3.23)
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("SurfR")):Aurora Maurizio, Anna Sofia Tascini. SurfR: Surface Protein Prediction and Identification. doi:10.18129/B9.bioc.SurfR, R package version 1.8.0, https://bioconductor.org/packages/SurfR.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | BatchEffect, DataImport, DifferentialExpression, FunctionalGenomics, FunctionalPrediction, GO, GeneExpression, GenePrediction, GeneSetEnrichment, Pathways, PrincipalComponent, RNASeq, Sequencing, Software, Transcription, Visualization |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 years) |
| 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
| Suggests | BiocStyle, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SurfR_1.8.0.tar.gz |
| Windows Binary (x86_64) | SurfR_1.8.0.zip |
| macOS Binary (big-sur-x86_64) | SurfR_1.8.0.tgz |
| macOS Binary (sonoma-arm64) | SurfR_1.8.0.tgz |
| 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/ |
| Package Downloads Report | Download Stats |