Package index • scatools

All functions

EM2(): Iterative phasing and theta_hat estimation

add_gc_cor(): Add GC correction to SCE Object

add_gc_freq(): Add GC frequency

add_hmmcopy(): Add HMMCopy results to sce object

bin_atac_frags(): Bin atac fragments

bin_frags_chr(): Bin scATAC fragments

bin_snp_data(): Bin SNPs into genomic segments

bin_snp_data2(): Bin SNP Data

bind_sublist(): Bind sublists within lists

bins_10mb: 10mb Bins for HG38

calc_ai(): Calculate allelic imbalance

calc_allelic(): Calculate allelic information over cells and bins

calc_clonal_diversity(): Calculate clonal diversity

calc_cnv_score(): Calculate CNV Score

calc_snn_specificity(): Calculate SNN Specificity

cluster_seurat(): Cluster using Seurat

cnaHeatmap() cloneCnaHeatmap(): Plot copy number heatmap

correct_atac_bias(): Correct ATAC Bias

disjoint_bins_map(): Map between bins

do_qc(): Basic QC

filter_sce(): Bin and/or Cell-wise quality filtering

gc_cor_modal(): Modal regression GC Correction for single cell data

gc_modal_qc_filter(): GC modal QC filter

get_assay_dat(): Utility to pull assay data and merge with features

get_blacklist(): Get blacklist regions

get_chr_arm_bins(): Get chromosome arm bins

get_cytobands(): Get genome cytobands

get_f_idx(): Get factor indices

get_gene_copy(): Get Gene Copies

get_ideal_mat() add_ideal_mat(): Get ideal bin matrix

get_snp_bidx(): Get SNP bin idx

get_snp_counts(): get_snp_counts

get_tiled_bins(): Get tiled bins

grab_hmm_res(): Grab HMM results from returned list

hmmcopy_singlecell(): Single Cell HMMcopy

identify_normal(): Identify normal cells from scATAC data

integrate_segments(): Integrate segments between assays

is_ideal_bin(): Flag ideal bins

leiden_wrapper(): Wrapper for the Leiden Algorithm

length_normalize(): Length normalize counts

load_atac_bins(): Load atac binned depth data

logNorm(): logNorm()

logr_col_fun(): Log Ratio Colors

merge_segments(): Merge segment levels

overlap_genes(): Overlap genes with bins

params_sc_hmm(): Single Cell HMMcopy parameters

perform_gc_cor(): Perform GC Correction

phase_snps(): EM phasing of SNPs

plot_cell_cna(): Plot Cell Copy Number

plot_cell_multi(): Plot multiple cell assays together

plot_cell_psuedobulk_cna(): Plot Psuedobulk cell CNA profiles

plot_clone_comp(): Clone Copy Number Comparison Plot

plot_gene_cna(): Plot Gene CNA

plot_segs(): Plot data with segments

pseudo_groups(): Pseudobulk groups

pseudo_join(): Join SNP and scATAC depth

pseudobulk_sce(): Pseudobulk cell CNA profiles

read_vartrix(): Read Vatrix Data

rebin_sce(): Rebin SingleCellExperiment object

run_sc_hmmcopy(): Single Cell HMMcopy

run_scatools(): Run scATAC Copy Number Analysis

scale_sub(): Scale and subset SCE assays

segment_cnv(): scATAC CBS CNV segmentation

smooth_counts(): Smooth outlier copy number counts

summarise_chr_arm(): Summarise copy number signal over chromosome arms

test_sce: Processed scATAC dataset