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Version

Version

1.3.3

License

BSD_3_clause + file LICENSE

Issues

221

Pull Requests

4

Stars

605

Forks

170

Maintainer

Christophe Georgescu

Last Published

August 25th, 2021

Functions in infercnv (1.3.3)

filterHighPNormals

filterHighPNormals: Filter the HMM identified CNV's by the CNV's posterior probability of belonging to a normal state.
HMM_states

infercnv object result of the processing of run() in the HMM example, to be used for other examples.
mcmc_obj

infercnv object result of the processing of inferCNVBayesNet in the example, to be used for other examples.
plot_cnv

Plot the matrix as a heatmap, with cells as rows and genes as columns, ordered according to chromosome
infercnv-class

The infercnv Class
inferCNVBayesNet

inferCNVBayesNet: Run Bayesian Network Mixture Model To Obtain Posterior Probabilities For HMM Predicted States
genes

Downsampled gene coordinates file from GrCh37
annots

Generated classification for 10 normal cells and 10 tumor cells.
apply_median_filtering

apply_median_filtering
plot_per_group

plot_per_group
run

run() : Invokes a routine inferCNV analysis to Infer CNV changes given a matrix of RNASeq counts.
validate_infercnv_obj

validate_infercnv_obj()
sample_object

sample_object
color.palette

Helper function allowing greater control over the steps in a color palette.
data

Generated SmartSeq2 expression data with 10 normal cells and 10 tumor cells. This is only to demonstrate how to use methods, not actual data to be used in an analysis.
infercnv-package

infercnv: Infer Copy Number Variation from Single-Cell RNA-Seq Data
infercnv_obj

infercnv object result of the processing of run() in the example, to be used for other examples.
MCMC_inferCNV-class

MCMC_inferCNV class
CreateInfercnvObject

CreateInfercnvObject
add_to_seurat

add_to_seurat()