# Tools for managing SingleCellExperiment objects as projects

## 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