SurfR
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 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 | 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 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 |
Old Source Packages for BioC 3.19 | Source Archive |