Package index • chevreulProcess

All functions

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