Package: SurfR 1.9.0

Aurora Maurizio

SurfR: Surface Protein Prediction and Identification

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.

Authors:Aurora Maurizio [aut, cre], Anna Sofia Tascini [aut, ctb]

SurfR_1.9.0.tar.gz
SurfR_1.9.0.zip(r-4.7)SurfR_1.9.0.zip(r-4.6)SurfR_1.9.0.zip(r-4.5)
SurfR_1.9.0.tgz(r-4.6-any)SurfR_1.9.0.tgz(r-4.5-any)
SurfR_1.9.0.tar.gz(r-4.7-any)SurfR_1.9.0.tar.gz(r-4.6-any)
SurfR_1.9.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SurfR/json (API)

# Install 'SurfR' in R:

install.packages('SurfR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/auroramaurizio/surfr/issues

Datasets:

countData - CountData
enrichedList - EnrichedList
ind_deg - Ind_deg
metadata - Metadata

On BioConductor:SurfR-1.9.0(bioc 3.24)SurfR-1.8.0(bioc 3.23)

software sequencing rnaseq geneexpression transcription differentialexpression principalcomponent genesetenrichment pathways batcheffect functionalgenomics visualization dataimport functionalprediction geneprediction go dge enrichment-analysis metaanalysis plots proteins public-data surface surfaceome

5.26 score 6 stars 5 scripts 17 exports 173 dependencies

Last updated from:b697ac2b0c. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	262
linux-devel-x86_64	NOTE	412
source / vignettes	OK	321
linux-release-x86_64	NOTE	433
macos-release-arm64	NOTE	219
macos-oldrel-arm64	NOTE	206
windows-devel	NOTE	333
windows-release	NOTE	318
windows-oldrel	NOTE	306
wasm-release	OK	257

Exports:Annotate_SPID combine_fisher_invnorm DGE DownloadArchS4 Enrichment Enrichment_barplot enrichr enrichr_download Gene2SProtein GEOmetadata listEnrichrDbs metaRNAseq plotPCA setEnrichrSite Splot SVenn TCGA_download

Dependencies:abind ade4 admisc AnnotationDbi ape askpass assertr backports base64enc BH Biobase BiocFileCache BiocGenerics biocmake BiocParallel biomaRt biomformat Biostrings bit bit64 blob bslib cachem checkmate cli clipr cluster codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray DESeq2 digest dir.expiry doParallel downloader dplyr dynamicTreeCut edgeR evaluate farver fastcluster fastmap filelock fitdistrplus fontawesome foreach foreign formatR Formula fs futile.logger futile.options generics GenomicRanges ggplot2 ggrepel glue gridExtra gtable highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 igraph impute IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise metaRNASeq mgcv mime multtest mvtnorm nlme nnet openssl openxlsx permute phyloseq pillar pixmap pkgconfig plyr png preprocessCore prettyunits progress purrr R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppArmadillo readr reshape2 rhdf5 rhdf5filters Rhdf5lib rjson rlang rmarkdown rpart RSQLite rstudioapi rvest S4Arrays S4Vectors S7 sass scales selectr Seqinfo SingleCellExperiment snow sp SparseArray SPsimSeq statmod stringi stringr SummarizedExperiment survival sys TCGAbiolinks TCGAbiolinksGUI.data tibble tidyr tidyselect tinytex tzdb utf8 vctrs vegan venn viridisLite vroom WGCNA withr xfun XML xml2 XVector yaml zip

Introduction to SurfR

Rendered fromIntro_to_SurfR.Rmdusingknitr::rmarkdown

Last update: 2024-12-12
Started: 2022-12-05

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Annotate_SPID	Annotate_SPID
combine_fisher_invnorm	combine_fisher_invnorm
countData	countData
DGE function	DGE
DownloadArchS4 function	DownloadArchS4
enrichedList	enrichedList
Enrichment function	Enrichment
Enrichment_barplot	Enrichment_barplot
Gene enrichment using Enrichr	enrichr
Download data from enrichr in the form of a named list - function from hypeR	enrichr_download
Gene2SProtein function	Gene2SProtein
GEOmetadata function	GEOmetadata
Check if EnrichR is online	getEnrichr
ind_deg	ind_deg
Look up available databases on Enrichr	listEnrichrDbs
metadata	metadata
metaRNAseq function	metaRNAseq
plotPCA function	plotPCA
Set Enrichr Website	setEnrichrSite
Splot function	Splot
SVenn	SVenn
TCGA_download function	TCGA_download