SurfR

Surface Protein Prediction and Identification

Bioconductor version: 3.23 · Package version: 1.8.0

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SurfR")

Details

Maintainer	Aurora Maurizio <auroramaurizio1@gmail.com>
Author	Aurora Maurizio [aut, cre] (ORCID: <https://orcid.org/0000-0002-7194-4637>), Anna Sofia Tascini [aut, ctb] (ORCID: <https://orcid.org/0000-0001-5731-5490>)
License	GPL-3 + file LICENSE
URL	https://github.com/auroramaurizio/SurfR
Bug Reports	https://github.com/auroramaurizio/SurfR/issues
Downloads rank	190
Source branch	RELEASE_3_23
biocViews	BatchEffect, DataImport, DifferentialExpression, FunctionalGenomics, FunctionalPrediction, GO, GeneExpression, GenePrediction, GeneSetEnrichment, Pathways, PrincipalComponent, RNASeq, Sequencing, Software, Transcription, Visualization

Documentation

Introduction to SurfR

Download

Source package

Dependencies

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

Suggests: BiocStyle, testthat (>= 3.0.0)