Tools for managing SingleCellExperiment objects as projects

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Documentation for package ‘chevreulProcess’ version 1.0.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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