Package: ssdGSA 0.1.1

Xingpeng Li

ssdGSA: Single Sample Directional Gene Set Analysis

A method that inherits the standard gene set variation analysis (GSVA) method and also provides the option to use summary statistics from any analysis (disease vs healthy, lesional side vs nonlesional side, etc..) input to define the direction of gene sets used for directional gene set score calculation for a given disease. Note to use this package, GSVA(>= 1.52.1) is needed to pre-installed. Hanzelmann, S., Castelo, R., and Guinney, J. (2013) <doi:10.1186/1471-2105-14-7>.

Authors:Xingpeng Li [aut, cre], Qi Qian [aut]

ssdGSA_0.1.1.tar.gz
ssdGSA_0.1.1.tar.gz(r-4.5-noble)ssdGSA_0.1.1.tar.gz(r-4.4-noble)
ssdGSA_0.1.1.tgz(r-4.4-emscripten)ssdGSA_0.1.1.tgz(r-4.3-emscripten)
ssdGSA.pdf |ssdGSA.html✨
ssdGSA/json (API)

# Install 'ssdGSA' in R:

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

Datasets:

data_matrix - This is data to be included in package
data_matrix_entrezID - This is data to be included in package
direction_matrix - This is data to be included in package
gene_sets - This is data to be included in package

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

3 exports 0.09 score 153 dependencies 3 scripts 246 downloads

Last updated 1 months agofrom:e8fd36825c. Checks:OK: 2. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Aug 27 2024
R-4.5-linux	OK	Aug 27 2024

Exports:ssdGSA ssdGSA_individual transform_ensembl_2_entrez

Dependencies:abind annotate AnnotationDbi ape aplot askpass beachmat BH Biobase BiocFileCache BiocGenerics BiocParallel BiocSingular Biostrings bit bit64 blob cachem cli clusterProfiler codetools colorspace cowplot cpp11 crayon curl data.table DBI dbplyr DelayedArray DelayedMatrixStats digest DOSE dplyr enrichplot fansi farver fastmap fastmatch fgsea filelock formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggforce ggfun ggnewscale ggplot2 ggplotify ggraph ggrepel ggtree glue GO.db GOSemSim graph graphlayouts gridExtra gridGraphics GSEABase gson GSVA gtable HDF5Array httr igraph IRanges irlba isoband jsonlite KEGGREST labeling lambda.r lattice lazyeval lifecycle magick magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl org.Hs.eg.db patchwork pillar pkgconfig plogr plyr png polyclip purrr qvalue R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp RcppArmadillo RcppEigen reshape2 rhdf5 rhdf5filters Rhdf5lib rjson rlang RSQLite rsvd S4Arrays S4Vectors ScaledMatrix scales scatterpie shadowtext SingleCellExperiment snow SparseArray sparseMatrixStats SpatialExperiment stringi stringr SummarizedExperiment sys systemfonts tibble tidygraph tidyr tidyselect tidytree treeio tweenr UCSC.utils utf8 vctrs viridis viridisLite withr XML xtable XVector yulab.utils zlibbioc

Single Sample Directional Gene Set Analysis (ssdGSA)

Rendered fromssdGSA.Rmdusingknitr::rmarkdownon Aug 27 2024.

Last update: 2024-07-23
Started: 2024-07-23

Help page	Topics
Function to Calculate the Average of Gene Expressions	avg_expression
Function to Check if Gene IDs in the Input Gene Data Match Well	check_gene_name_match
Function to Check if Gene IDs in the Input Gene Data Match Well When Direction Matrix Is Missing	check_gene_name_match_noDir
Function to Check if Genes in Gene Sets Have Missing Information in Data Matrix and Direction Matrix	check_genes_missing
Function to Check if Genes in Gene Sets Have Missing Information in Data Matrix	check_genes_missing_noDir
Function to Check if 100% of Genes in Gene Sets Have Missing Information in Data Matrix	check_genes_missing_total
This is data to be included in package	data_matrix
This is data to be included in package	data_matrix_entrezID
This is data to be included in package	direction_matrix
This is data to be included in package	gene_sets
Function to Calculate Median of Gene Expressions	median_expression
Single Sample Directional Gene Set Analysis (ssdGSA)	ssdGSA
Single Sample Directional Gene Set Analysis Using Individual Weighted Scores	ssdGSA_individual
Function to Calculate Single Sample Gene Set Scores without Direction Matrix	ssGSA
Function to Transform ENSEMBL ID to ENTREZ ID	transform_ensembl_2_entrez

Package: ssdGSA 0.1.1

ssdGSA: Single Sample Directional Gene Set Analysis

Single Sample Directional Gene Set Analysis (ssdGSA)

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Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)