Package: chevreulProcess 0.99.23

chevreulProcess: Tools for managing SingleCellExperiment objects as projects

Tools analyzing SingleCellExperiment objects as projects. for input into the Chevreul app downstream. Includes functions for analysis of single cell RNA sequencing data. Supported by NIH grants R01CA137124 and R01EY026661 to David Cobrinik.

Authors:Kevin Stachelek [aut, cre], Bhavana Bhat [aut]

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chevreulProcess.pdf |chevreulProcess.html✨
chevreulProcess/json (API)
NEWS

# Install 'chevreulProcess' in R:

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

Bug tracker:https://github.com/cobriniklab/chevreulprocess/issues

Pkgdown site:https://cobriniklab.github.io

Datasets:

cc.genes.cyclone - Cyclone cell cycle pairs by symbol
ensembl_version - Ensembl version used for build
grch38 - Human annotation data
grch38_tx2gene - Human transcripts to genes
human_to_mouse_homologs - Gene Homologs Between Human and Mouse
small_example_dataset - Small example SingleCellExperiment
tiny_sce - Tiny example SingleCellExperiment

On CRAN:

coverage rnaseq sequencing visualization geneexpression transcription singlecell transcriptomics normalization preprocessing qualitycontrol dimensionreduction dataimport

3.18 score 2 scripts 22 exports 186 dependencies

Last updated 2 months agofrom:9a49061a3c. Checks:1 OK, 5 WARNING. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 26 2025
R-4.5-win	WARNING	Jan 26 2025
R-4.5-mac	WARNING	Jan 26 2025
R-4.5-linux	WARNING	Jan 26 2025
R-4.4-win	WARNING	Jan 26 2025
R-4.4-mac	WARNING	Jan 26 2025

Exports:find_all_markers genes_to_transcripts get_colData get_feature_types get_features get_variable_features integration_workflow load_bigwigs propagate_spreadsheet_changes query_experiment record_experiment_data regress_cell_cycle reintegrate_sce sce_calcn sce_cluster sce_de sce_integrate sce_process set_colData set_feature_type splitByCol transcripts_to_genes

Dependencies:abind AnnotationDbi AnnotationFilter askpass assorthead batchelor beachmat beeswarm BH Biobase BiocGenerics BiocIO BiocNeighbors BiocParallel BiocSingular Biostrings bit bit64 bitops blob bluster brio cachem Cairo callr circlize cli clipr cluster cmdfun codetools colorspace cpp11 crayon credentials curl DBI DelayedArray DelayedMatrixStats desc diffobj digest dplyr dqrng edgeR EnsDb.Hsapiens.v86 ensembldb evaluate fansi farver fastmap FNN formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges gert ggbeeswarm ggplot2 ggrastr ggrepel gh gitcreds GlobalOptions glue gridExtra gtable hms httr httr2 igraph ini IRanges irlba isoband jsonlite KEGGREST labeling lambda.r lattice lazyeval lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats megadepth memoise metapod mgcv mime munsell nlme openssl pheatmap pillar pkgbuild pkgconfig pkgload plogr png praise prettyunits processx progress ProtGenerics ps purrr R.methodsS3 R.oo R.utils R6 ragg rappdirs RColorBrewer Rcpp RcppAnnoy RcppEigen RcppML RcppProgress RCurl readr ResidualMatrix restfulr Rhtslib rjson rlang rprojroot Rsamtools RSpectra RSQLite rstudioapi rsvd rtracklayer Rtsne S4Arrays S4Vectors ScaledMatrix scales scater scran scuttle shape SingleCellExperiment sitmo snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment sys systemfonts testthat textshaping tibble tidyr tidyselect tzdb UCSC.utils usethis utf8 uwot vctrs vipor viridis viridisLite vroom waldo whisker withr xfun XML XVector yaml zip

chevreulProcess

Kevin Stachelek, Bhavana Bhat

Rendered fromchevreulProcess.Rmdusingknitr::rmarkdownon Jan 26 2025.

Last update: 2024-12-26
Started: 2024-10-23

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Annotate percent mitochondrial reads per cell	add_percent_mito
Annotate Cell Cycle	annotate_cell_cycle
Update a database of chevreul projects	append_to_project_db
Create a database of bigwigfiles	build_bigwig_db
Cyclone cell cycle pairs by symbol	cc.genes.cyclone
Clustering Workflow	clustering_workflow
Convert SingleCellExperiment Objects from Human to Mouse	convert_human_sce_to_mouse
Convert gene symbols between mouse and human	convert_symbols_by_species
Create a database of chevreul projects	create_project_db
Ensembl version used for build	ensembl_version
Find All Markers	find_all_markers
Gene Symbols to Ensembl Transcript Ids	genes_to_transcripts
Get cell metadata from a given object	get_colData
Get Feature Types	get_feature_types
Get feature names	get_features
Get object metadata	get_sce_metadata
Get Transcripts in object	get_transcripts_from_sce
Get variable features	get_variable_features
Human annotation data	grch38
Human transcripts to genes	grch38_tx2gene
Gene Homologs Between Human and Mouse	human_to_mouse_homologs
Batch Correct Multiple Single Cell Objects	integrate
Integration Workflow	integration_workflow
Load Bigwigs	load_bigwigs
Load SingleCellExperiment Files from a single project path	load_sce_from_proj
Read in Gene and Transcript SingleCellExperiment Objects	load_sce_path
Make Bigwig Database	make_bigwig_db
Merge Small SingleCellExperiment Objects	merge_small_sces
Retrieve Metadata from Batch	metadata_from_batch
Propagate Metadata Changes	propagate_spreadsheet_changes
Query Experiment	query_experiment
Read a database of chevreul projects	read_project_db
Record Experiment Metadata	record_experiment_data
Regress SingleCellExperiment Object by Given Set of Genes	regress_cell_cycle
Reintegrate (filtered) SingleCellExperiment objects	reintegrate_sce
Retrieve Assay	retrieve_experiment
Save object to /output/sce/_sce.rds	save_sce
Calculate Read Count Metrics for a object	sce_calcn
Run Louvain Clustering at Multiple Resolutions	sce_cluster
Run Differential Expression	sce_de
Run SingleCellExperiment Integration	sce_integrate
Preprocess Single Cell Object	sce_preprocess
Run SingleCellExperiment Pipeline	sce_process
Dimensional Reduction	sce_reduce_dimensions
Set cell metadata	set_colData
Set Feature Types	set_feature_type
Small example SingleCellExperiment	small_example_dataset
Split SingleCellExperiment by colData variable	splitByCol
Stash Marker Genes in a SingleCellExperiment Object	stash_marker_features
Subset by new colData	subset_by_colData
Tiny example SingleCellExperiment	tiny_sce
Ensembl Transcript Ids to Gene Symbols	transcripts_to_genes
Update a database of chevreul projects	update_project_db