Man pages for ChromSCape
Analysis of single-cell epigenomics datasets with a Shiny App

annotation_from_merged_peaksFind nearest peaks of each gene and return refined annotation
anocol_binaryHelper binary column for anocol function
anocol_categoricalHelper binary column for anocol function
bams_to_matrix_indexesCount bam files on interval to create count indexes
beds_to_matrix_indexesCount bed files on interval to create count indexes
call_macs2_merge_peaksCalling MACS2 peak caller and merging resulting peaks
check_correct_datamatrixCheck if matrix rownames are well formated and correct if...
choose_cluster_scExpChoose a number of clusters
choose_perplexityChoose perplexity depending on number of cells for Tsne
colors_scExpAdding colors to cells & features
combine_datamatrixCombine two matrices and emit warning if no regions are in...
combine_enrichmentTestsRun enrichment tests and combine into list
CompareedgeRGLMCreates a summary table with the number of genes under- or...
consensus_clustering_scExpWrapper to apply ConsensusClusterPlus to scExp object
correlation_and_hierarchical_clust_scExpCorrelation and hierarchical clustering
create_sample_name_matCreate a sample name matrix
create_scDataset_rawCreate a simulated single cell datamatrix & cell annotation
create_scExpWrapper to create the single cell experiment from count...
DA_one_vs_rest_funDifferential Analysis in 'One vs Rest' mode
DA_pairwiseRun differential analysis in Pairwise mode
define_featureDefine the features on which reads will be counted
detect_samplesHeuristic discovery of samples based on cell labels
differential_analysis_scExpRuns differential analysis between cell clusters
exclude_features_scExpRemove specific features (CNA, repeats)
feature_annotation_scExpAdd gene annotations to features
filter_correlated_cell_scExpFilter lowly correlated cells
filter_genes_with_refined_peak_annotationFilter genes based on peak calling refined annotation
filter_scExpFilter cells and features
generate_count_matrixGenerate count matrix
generate_feature_namesGenerate feature names
gene_set_enrichment_analysis_scExpRuns Gene Set Enrichment Analysis on genes associated with...
get_color_dataframe_from_inputGet color dataframe from shiny::colorInput
get_genomic_coordinatesGet SingleCellExperiment's genomic coordinates
has_genomic_coordinatesDoes SingleCellExperiment has genomic coordinates in features...
hg38.chromosomesData.frame of chromosome length - hg38
hg38.GeneTSSData.frame of gene TSS - hg38
import_count_input_filesImport and count input files depending on their format
import_scExpRead single-cell matrix(ces) into scExp
index_peaks_barcodes_to_matrix_indexesRead index-peaks-barcodes trio files on interval to create...
launchAppLaunch ChromSCape
load_MSIGdbLoad and format MSIGdb pathways using msigdbr package
merge_MACS2_peaksMerge peak files from MACS2 peak caller
mm10.chromosomesData.frame of chromosome length - mm10
mm10.GeneTSSData.frame of gene TSS - mm10
normalize_scExpNormalize counts
num_cell_after_cor_filt_scExpNumber of cells before & after correlation filtering
num_cell_after_QC_filt_scExpTable of cells before / after QC
num_cell_before_cor_filt_scExpTable of number of cells before correlation filtering
num_cell_in_cluster_scExpNumber of cells in each cluster
num_cell_scExpTable of cells
pca_irlba_for_sparseMatrixRun sparse PCA using irlba SVD
peaks_to_binsTransforms a peaks x cells count matrix into a bins x cells...
plot_cluster_consensus_scExpPlot cluster consensus
plot_differential_H1_scExpDifferential H1 distribution plot
plot_differential_summary_scExpDifferential summary barplot
plot_differential_volcano_scExpVolcano plot of differential features
plot_distribution_scExpPlotting distribution of signal
plot_heatmap_scExpPlot cell correlation heatmap with annotations
plot_reduced_dim_scExpPlot reduced dimensions (PCA, TSNE, UMAP)
preprocess_CPMPreprocess scExp - Counts Per Million (CPM)
preprocess_feature_size_onlyPreprocess scExp - size only
preprocess_RPKMPreprocess scExp - Read per Kilobase Per Million (RPKM)
preprocess_TPMPreprocess scExp - Transcripts per Million (TPM)
raw_counts_to_feature_count_filesCreate a sparse count matrix from various format of input...
read_count_mat_with_separated_chr_start_endRead a count matrix with three first columns (chr,start,end)
reduce_dim_batch_correctionReduce dimension with batch corrections
reduce_dims_scExpReduce dimensions (PCA, TSNE, UMAP)
remove_chr_M_funRemove chromosome M from scExprownames
remove_non_canonical_funRemove non canonical chromosomes from scExp
results_enrichmentTestResutls of hypergeometric gene set enrichment test
run_pairwise_testsRun pairwise tests
run_tsne_scExpRun tsne on single cell experiment
scExpA SingleCellExperiment outputed by ChromSCape
separate_BAM_into_clustersSeparate BAM files into cell cluster BAM files
separator_count_matDetermine Count matrix separator ("tab" or ",")
subsample_scExpSubsample scExp
subset_bam_call_peaksPeak calling on cell clusters
table_enriched_genes_scExpCreates table of enriched genes sets
warning_DAWarning for differential_analysis_scExp
warning_plot_reduced_dim_scExpA warning helper for plot_reduced_dim_scExp
warning_raw_counts_to_feature_count_filesWarning for _raw_counts_to_feature_count_files
ChromSCape documentation built on Nov. 8, 2020, 6:57 p.m.