Package: chevreulProcess 0.99.1

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

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

2.00 score 3 scripts 28 exports 222 dependencies

Last updated 8 hours agofrom:21fcd9e9d2. Checks:ERROR: 5. Indexed: yes.

Target	Result	Date
Doc / Vignettes	FAIL	Oct 29 2024
R-4.5-win	ERROR	Oct 29 2024
R-4.5-linux	ERROR	Oct 29 2024
R-4.4-win	ERROR	Oct 29 2024
R-4.4-mac	ERROR	Oct 29 2024

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

Dependencies:abind annotate AnnotationDbi AnnotationFilter AnnotationHub askpass assorthead batchelor beachmat beeswarm BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocNeighbors BiocParallel BiocSingular BiocVersion Biostrings bit bit64 bitops blob bluster brio cachem Cairo callr chevreuldata circlize cli clipr cluster cmdfun codetools colorspace cowplot cpp11 crayon credentials curl DBI dbplyr DelayedArray DelayedMatrixStats desc diffobj digest dplyr dqrng edgeR EnhancedVolcano EnrichmentBrowser EnsDb.Hsapiens.v86 EnsDb.Mmusculus.v79 ensembldb evaluate ExperimentHub fansi farver fastmap filelock FNN forcats formatR fs futile.logger futile.options future generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges gert ggbeeswarm ggplot2 ggrastr ggrepel gh gitcreds GlobalOptions globals glue GO.db graph graphite gridExtra GSEABase gtable harmony hms httr httr2 hwriter igraph ini IRanges irlba isoband jsonlite KEGGgraph KEGGREST labeling lambda.r lattice lazyeval lifecycle limma listenv locfit magrittr MASS Matrix MatrixGenerics matrixStats megadepth memoise metapod mgcv mime munsell nlme openssl org.Hs.eg.db parallelly pathview 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 RcppArmadillo RcppEigen RcppML RcppProgress RCurl readr rematch2 ResidualMatrix restfulr Rgraphviz RhpcBLASctl Rhtslib rjson rlang rprojroot Rsamtools RSpectra RSQLite rstudioapi rsvd rtracklayer Rtsne S4Arrays S4Vectors safe ScaledMatrix scales scater scran scuttle shape SingleCellExperiment sitmo snow SparseArray SparseM sparseMatrixStats SPIA 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 xtable XVector yaml zip zlibbioc

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

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
Give a new project name to a SingleCellExperiment object	rename_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