Package: ProjecTILs 3.7.0

Massimo Andreatta

ProjecTILs: Reference-based analysis of scRNA-seq data

This package implements methods to project single-cell RNA-seq data onto a reference atlas, enabling interpretation of unknown cell transcriptomic states in the the context of known, reference states.

Authors:Massimo Andreatta [aut, cre], Paul Gueguen [aut], Josep Garnica [aut], Santiago Carmona [aut]

ProjecTILs_3.7.0.tar.gz
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ProjecTILs.pdf |ProjecTILs.html✨
ProjecTILs/json (API)

# Install 'ProjecTILs' in R:

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

Bug tracker:https://github.com/carmonalab/projectils/issues

Datasets:

cell.cycle.obj - Cell cycling signatures
Hs2Mm.convert.table - Human-mouse ortholog conversion table
query_example_seurat - Test dataset for ProjecTILs

On CRAN:

6.72 score 315 stars 166 scripts 20 exports 174 dependencies

Last updated from:1159e17788. Checks:7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	NOTE	419
source / vignettes	OK	299
linux-release-x86_64	NOTE	397
macos-release-arm64	NOTE	236
macos-oldrel-arm64	NOTE	246
windows-devel	NOTE	367
windows-release	NOTE	514
windows-oldrel	NOTE	453
wasm-release	OK	248

Exports:cellstate.predict celltype.heatmap compute_silhouette find.discriminant.dimensions find.discriminant.genes FindAllMarkers.bygroup get.reference.maps list.reference.maps load.reference.map make.projection make.reference merge.Seurat.embeddings plot.discriminant.3d plot.projection plot.statepred.composition plot.states.radar ProjecTILs.classifier read.sc.query recalculate.embeddings Run.ProjecTILs

Dependencies:abind askpass assorthead base64enc beachmat BH Biobase BiocGenerics BiocNeighbors BiocParallel bitops bslib cachem caTools cli cluster codetools colorspace commonmark cowplot cpp11 crosstalk curl data.table DelayedArray deldir digest dotCall64 dplyr dqrng evaluate farver fastDummies fastmap fitdistrplus FNN fontawesome formatR fs futile.logger futile.options future future.apply generics GenomicRanges ggplot2 ggrepel ggridges globals glue goftest gplots gridExtra gtable gtools here highr htmltools htmlwidgets httpuv httr ica igraph IRanges irlba isoband jquerylib jsonlite KernSmooth knitr labeling lambda.r later lattice lazyeval lifecycle listenv lmtest magrittr MASS Matrix MatrixGenerics matrixStats memoise mime miniUI nlme openssl otel parallelly patchwork pbapply pheatmap pillar pkgconfig plotly plyr png polyclip pracma progressr promises purrr R.methodsS3 R.oo R.utils R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppProgress RcppTOML reshape2 reticulate rlang rmarkdown ROCR rprojroot RSpectra Rtsne S4Arrays S4Vectors S7 sass scales scattermore scGate sctransform Seqinfo Seurat SeuratObject shiny SingleCellExperiment sitmo snow sourcetools sp spam SparseArray spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils STACAS stringi stringr SummarizedExperiment survival sys tensor tibble tidyr tidyselect tinytex UCell umap utf8 uwot vctrs viridisLite withr xfun xtable XVector yaml zoo

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Cell cycling signatures	cell.cycle.obj
Predict cell states of a projected dataset	cellstate.predict
Plot a averaged expression heatmap from a Seurat object	celltype.heatmap
Calculate Silhouette coefficient	compute_silhouette
Find discriminant dimensions	find.discriminant.dimensions
Find discriminant genes	find.discriminant.genes
Gene expression markers shared by multiple groups of cells	FindAllMarkers.bygroup
Retrieve and load reference atlas	get.reference.maps
Human-mouse ortholog conversion table	Hs2Mm.convert.table
Available reference atlas for ProjecTILs	list.reference.maps
Load Reference Atlas	load.reference.map
Project a query scRNA-seq dataset onto a reference atlas	make.projection
Make a ProjecTILs reference	make.reference
Merge Seurat objects, including reductions (e.g. PCA, UMAP, ICA)	merge.Seurat.embeddings
3D plot of reference map with extra discriminant dimension	plot.discriminant.3d
Show UMAP projection of query on reference map	plot.projection
Summarize the predicted cell states of an object	plot.statepred.composition
Show expression level of key genes	plot.states.radar
Annotate query dataset using a reference object	ProjecTILs.classifier
Test dataset for ProjecTILs	query_example_seurat
Read to memory a query expression matrix	read.sc.query
Recalculate low dimensional embeddings after projection	recalculate.embeddings
Project a query scRNA-seq dataset onto a reference atlas	Run.ProjecTILs