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Version
Version
1.3.3
0.99.7
0.8.2
0.8.1
0.8
0.1
Version
0.8
License
BSD_3_clause + file LICENSE
Maintainer
Timothy Tickle
Last Published
August 25th, 2021
Functions in infercnv (0.8)
Search all functions
split_references
split_references()
subtract_ref_expr_from_obs
subtract_ref_expr_from_obs()
ngchm
ngchm() : generates next gen heatmap
get_average_bounds
get_average_bounds()
get_reference_grouped_cell_indices
get_reference_grouped_cell_indices()
infercnv-class
The infercnv Class
require_above_min_cells_ref
require_above_min_cells_ref()
require_above_min_mean_expr_cutoff
require_above_min_mean_expr_cutoff ()
run
run() : Invokes a routine inferCNV analysis to Infer CNV changes given a matrix of RNASeq counts.
transform_to_reference_based_Zscores
transform_to_reference_based_Zscores()
scale_cnv_by_spike
scale_cnv_by_spike()
make_zero_NA
make_zero_NA()
validate_infercnv_obj
validate_infercnv_obj()
mask_non_DE_genes_basic
mask_non_DE_genes_basic()
remove_outliers_norm
remove_outliers_norm()
remove_spike
remove_spike()
smooth_by_chromosome
smooth_by_chromosome()
spike_in_variation_chrs
spike_in_variation_chrs() Adds a 'SPIKE'-in to the observations set at different thresholds of loss/gain to aid in tracking the effect of infercnv operations and for defining the final scaling.
clear_noise_via_ref_mean_sd
clear_noise_via_ref_mean_sd()
compute_normalization_factor
compute_normalization_factor()
center_cell_expr_across_chromosome
center_cell_expr_across_chromosome()
clear_noise
clear_noise()
invert_log2xplus1
invert_log2xplus1()
log2xplus1
log2xplus1()
infercnv-package
infercnv: Infer Copy Number Variation from Single-Cell RNA-Seq Data
normalize_counts_by_seq_depth
normalize_counts_by_seq_depth()
invert_log2
invert_log2()
plot_cnv
Plot the matrix as a heatmap, with cells as rows and genes as columns, ordered according to chromosome
remove_genes
remove_genes()
remove_genes_at_ends_of_chromosomes
remove_genes_at_ends_of_chromosomes()
anscombe_transform
anscombe_transform()
apply_max_threshold_bounds
apply_max_threshold_bounds()
mean_center_gene_expr
mean_center_gene_expr()
CreateInfercnvObject
CreateInfercnvObject
get_DE_genes_basic
get_DE_genes_basic
Create_NGCHM
Create Next Generation Clustered Heat Map (NG-CHM)
