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_feature_types       Get Feature Types
get_features            Get feature names
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
