SurfR
Surface Protein Prediction and Identification
Bioconductor version: 3.24 · Package version: 1.9.0
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 | 325 |
| Source branch | devel |
| biocViews | BatchEffect, DataImport, DifferentialExpression, FunctionalGenomics, FunctionalPrediction, GO, GeneExpression, GenePrediction, GeneSetEnrichment, Pathways, PrincipalComponent, RNASeq, Sequencing, Software, Transcription, Visualization |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | SurfR_1.9.0.tar.gz |
| Windows binary (x86_64) | SurfR_1.9.0.zip |
| macOS binary (arm64) | SurfR_1.9.0.tgz |
| macOS binary (x86_64) | SurfR_1.9.0.tgz |
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)