Package: gsean 1.25.0

Dongmin Jung

gsean: Gene Set Enrichment Analysis with Networks

Biological molecules in a living organism seldom work individually. They usually interact each other in a cooperative way. Biological process is too complicated to understand without considering such interactions. Thus, network-based procedures can be seen as powerful methods for studying complex process. However, many methods are devised for analyzing individual genes. It is said that techniques based on biological networks such as gene co-expression are more precise ways to represent information than those using lists of genes only. This package is aimed to integrate the gene expression and biological network. A biological network is constructed from gene expression data and it is used for Gene Set Enrichment Analysis.

Authors:Dongmin Jung

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NEWS

# Install 'gsean' in R:

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

Datasets:

GO_dme - Gene Ontology terms with gene ID for Drosophila melanogaster
KEGG_hsa - KEGG pathways with gene symbol for human

On BioConductor:gsean-1.25.0(bioc 3.20)gsean-1.24.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

4 exports 0.61 score 108 dependencies

Last updated 2 months agofrom:aa9b841aa8

Exports:centrality_gsea exprs2adj gsean label_prop_gsea

Dependencies:AnnotationDbi askpass BH Biobase BiocFileCache BiocGenerics BiocParallel biomaRt Biostrings bit bit64 bitops blob cachem caTools chron cli codetools colorspace cowplot cpp11 crayon curl data.table DBI dbplyr digest dplyr fansi farver fastmap fastmatch fgsea filelock formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData ggplot2 glue gplots graph gsubfn gtable gtools hash hms httr httr2 igraph IRanges isoband jsonlite KEGGREST kernlab KernSmooth labeling lambda.r lattice lifecycle magrittr MASS Matrix memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr plotrix plyr png PPInfer prettyunits progress proto purrr R6 rappdirs RColorBrewer Rcpp rlang RSQLite S4Vectors scales snow sqldf STRINGdb stringi stringr sys tibble tidyr tidyselect UCSC.utils utf8 vctrs viridisLite withr xml2 XVector yeastExpData zlibbioc

Gene Set Enrichment Analysis with Networks

Dongmin Jung

Rendered fromgsean.Rmdusingknitr::rmarkdownon Jun 24 2024.

Last update: 2019-04-29
Started: 2018-01-07

Help page	Topics
Gene Set Enrichment Analysis with Networks	gsean-package
Gene Set Enrichment Analysis with centrality measure	centrality_gsea
Convert gene expression data to adjacency matrix by using correlation coefficients	exprs2adj
Gene Ontology terms with gene ID for Drosophila melanogaster	GO_dme
Gene Set Enrichment Analysis with Networks	gsean
KEGG pathways with gene symbol for human	KEGG_hsa
Over-representaion analysis with the label propagation algorithm	label_prop_gsea

Package: gsean 1.25.0

gsean: Gene Set Enrichment Analysis with Networks

Gene Set Enrichment Analysis with Networks

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Usage by other packages (reverse dependencies)