Package: scGOclust 0.2.1

Yuyao Song

scGOclust: Measuring Cell Type Similarity with Gene Ontology in Single-Cell RNA-Seq

Traditional methods for analyzing single cell RNA-seq datasets focus solely on gene expression, but this package introduces a novel approach that goes beyond this limitation. Using Gene Ontology terms as features, the package allows for the functional profile of cell populations, and comparison within and between datasets from the same or different species. Our approach enables the discovery of previously unrecognized functional similarities and differences between cell types and has demonstrated success in identifying cell types' functional correspondence even between evolutionarily distant species.

Authors:Yuyao Song [aut, cre, ctb], Irene Papatheodorou [aut, ths]

scGOclust_0.2.1.tar.gz
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scGOclust_0.2.1.tgz(r-4.4-any)scGOclust_0.2.1.tgz(r-4.3-any)
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scGOclust.pdf |scGOclust.html✨
scGOclust/json (API)

# Install 'scGOclust' in R:

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

Bug tracker:https://github.com/papatheodorou-group/scgoclust/issues

Datasets:

dme_subset - Drosophila gut scRNA-seq data, 10X Chromium Subset to 45 cells per cell type as an example data
dme_tbl - Drosophila EMSEMBL gene and GO annotation, subset to genes present in 'dme_subset'
mmu_subset - Mouse stomach and intestine scRNA-seq data, microwell-seq Subset to 50 cells per cell type as an example data
mmu_tbl - Mouse EMSEMBL gene and GO annotation, subset to genes present in 'mmu_subset'

On CRAN:

10 exports 8 stars 1.91 score 179 dependencies 14 scripts 201 downloads

Last updated 7 months agofrom:d014f36903. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 17 2024
R-4.5-win	OK	Sep 17 2024
R-4.5-linux	OK	Sep 17 2024
R-4.4-win	OK	Sep 17 2024
R-4.4-mac	OK	Sep 17 2024
R-4.3-win	OK	Sep 17 2024
R-4.3-mac	OK	Sep 17 2024

Exports:analyzeGOSeurat cellTypeGOCorr crossSpeciesCellTypeGOCorr ensemblToGo getCellTypeGO getCellTypeSharedGO getCellTypeSharedTerms makeGOSeurat plotCellTypeCorrHeatmap plotCellTypeSankey

Dependencies:abind AnnotationDbi askpass base64enc BH Biobase BiocFileCache BiocGenerics biomaRt Biostrings bit bit64 bitops blob bslib cachem caTools cli cluster codetools colorspace commonmark cowplot cpp11 crayon crosstalk curl data.table DBI dbplyr deldir digest dotCall64 dplyr dqrng evaluate fansi farver fastDummies fastmap filelock fitdistrplus FNN fontawesome fs future future.apply generics GenomeInfoDb GenomeInfoDbData ggplot2 ggrepel ggridges globals glue goftest gplots gridExtra gtable gtools here highr hms htmltools htmlwidgets httpuv httr httr2 ica igraph IRanges irlba isoband jquerylib jsonlite KEGGREST KernSmooth knitr labeling later lattice lazyeval leiden lifecycle limma listenv lmtest magrittr MASS Matrix matrixStats memoise mgcv mime miniUI munsell networkD3 nlme openssl parallelly patchwork pbapply pheatmap pillar pkgconfig plogr plotly plyr png polyclip pracma prettyunits progress progressr promises purrr R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppProgress RcppTOML reshape2 reticulate rlang rmarkdown ROCR rprojroot RSpectra RSQLite Rtsne S4Vectors sass scales scattermore sctransform Seurat SeuratObject shiny sitmo slanter sourcetools sp spam spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils statmod stringi stringr survival sys tensor tibble tidyr tidyselect tinytex UCSC.utils utf8 uwot vctrs viridisLite withr xfun xml2 xtable XVector yaml zlibbioc zoo

scGOclust_vignette

Rendered fromscGOclust_vignette.Rmdusingknitr::rmarkdownon Sep 17 2024.

Last update: 2023-11-24
Started: 2023-09-30

Help page	Topics
standard seurat analysis on GO_seurat object	analyzeGOSeurat
calculate correlation between cell types represented by scaled GO, per-species	cellTypeGOCorr
calculate cross-species correlation between cell types represented by scaled GO	crossSpeciesCellTypeGOCorr
Drosophila gut scRNA-seq data, 10X Chromium Subset to 45 cells per cell type as an example data	dme_subset
Drosophila EMSEMBL gene and GO annotation, subset to genes present in `dme_subset`	dme_tbl
get requested ensembl ID to GO mapping table	ensemblToGo
get per cell type average scaled vector of GO terms	getCellTypeGO
get shared up and down regulated GO terms for all pairs of cell types	getCellTypeSharedGO
query co-up and co-down regulated GO terms from certain cell type pairs	getCellTypeSharedTerms
record some global variables: pre-defined column name in biomaRt query and markers	globalvariables
create a seurat object with GO terms	makeGOSeurat
Mouse stomach and intestine scRNA-seq data, microwell-seq Subset to 50 cells per cell type as an example data	mmu_subset
Mouse EMSEMBL gene and GO annotation, subset to genes present in `mmu_subset`	mmu_tbl
plot clustered heatmap for cell type corr	plotCellTypeCorrHeatmap
plot Sankey diagram for cell type links above a certain threshould	plotCellTypeSankey

Package: scGOclust 0.2.1

scGOclust: Measuring Cell Type Similarity with Gene Ontology in Single-Cell RNA-Seq

scGOclust_vignette

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