SurfR
This is the development version of SurfR; for the stable release version, see SurfR.
Surface Protein Prediction and Identification
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 1.9.0 |
| 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 |
Package Archives
Follow 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 (big-sur-x86_64) | SurfR_1.9.0.tgz |
| macOS Binary (sonoma-arm64) | SurfR_1.9.0.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 |