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("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 | ||
| NEWS | Text | |
| LICENSE | Text |
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 |
See More
| Suggests | testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| 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 [email protected]: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 |