BEARscc (Bayesian ERCC Assesstment of Robustness of Single Cell Clusters)

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Documentation for package ‘BEARscc’ version 1.12.0

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BEARscc-package BEARscc (Bayesian ERCC Assesstment of Robustness of Single Cell Clusters)
. Reports BEARscc metrics for cells.
.Random.seed BEARscc downstream example objects.
analysis_examples BEARscc downstream example objects.
apply_bayes Estimates noise in single cell data.
BEARscc BEARscc (Bayesian ERCC Assesstment of Robustness of Single Cell Clusters)
BEARscc_clusts.df BEARscc downstream example objects.
BEARscc_examples Example data for BEARscc.
BEAR_analyzed.sce BEARscc downstream example objects.
BEAR_examples.sce Example data for BEARscc.
build_dropoutmodel Estimates noise in single cell data.
calculate_cell_metrics Reports BEARscc metrics for cells.
calculate_cell_metrics_by_cluster Reports BEARscc metrics for cells.
calculate_cluster_metrics Reports BEARscc metrics for clusters.
calculate_cluster_metrics_by_cluster Reports BEARscc metrics for clusters.
cleanup_model_names Estimates noise in single cell data.
clusters.df BEARscc downstream example objects.
cluster_consensus Cluster the consensus matrix.
compute_alpha Estimates noise in single cell data.
compute_consensus Compute consensus matrix.
compute_genewise_dropouts Estimates noise in single cell data.
counts2mpc Estimates noise in single cell data.
create_cm Compute consensus matrix.
create_null_dropout_model Estimates noise in single cell data.
data.counts.df Example data for BEARscc.
ERCC.counts.df Example data for BEARscc.
ERCC.meta.df Example data for BEARscc.
estimate_missingdata Estimates noise in single cell data.
estimate_mu2sigma Estimates noise in single cell data.
estimate_noiseparameters Estimates noise in single cell data.
estimate_undetected2molpercell Estimates noise in single cell data.
example_code Computes 'BEARscc' simulated technical replicates.
execute_noiseinjected_counts Computes 'BEARscc' simulated technical replicates.
execute_sim_replicates Computes 'BEARscc' simulated technical replicates.
fill_out_count_probability_table Computes 'BEARscc' simulated technical replicates.
genewise_dropouts Computes 'BEARscc' simulated technical replicates.
gene_name Computes 'BEARscc' simulated technical replicates.
HPC_simulate_replicates Computes 'BEARscc' simulated technical replicates.
iterate_alphas Estimates noise in single cell data.
iterate_spikeins Estimates noise in single cell data.
L1 Reports BEARscc metrics for clusters.
mean.prom Reports BEARscc metrics for clusters.
melt_spikeins Estimates noise in single cell data.
noise_consensus BEARscc downstream example objects.
Overall.mean Reports BEARscc metrics for clusters.
permute_count_in_dropout_range Computes 'BEARscc' simulated technical replicates.
plot_alpha2mu Estimates noise in single cell data.
plot_cluster_metrics Reports BEARscc metrics for clusters.
plot_mu2sigma Estimates noise in single cell data.
plot_obs2actual Estimates noise in single cell data.
plot_spikein_fits Estimates noise in single cell data.
prepare_data Estimates noise in single cell data.
randomizer Computes 'BEARscc' simulated technical replicates.
recluster BEARscc downstream example objects.
report_cell_metrics Reports BEARscc metrics for cells.
report_cluster_metrics Reports BEARscc metrics for clusters.
rn Reports BEARscc metrics for cells.
sample_models Estimates noise in single cell data.
simulate_replicates Computes 'BEARscc' simulated technical replicates.
size Reports BEARscc metrics for clusters.
subcompute_sample_models Estimates noise in single cell data.
subplot_spikein_fits Estimates noise in single cell data.
transcripts Estimates noise in single cell data.
V1 Estimates noise in single cell data.
value Reports BEARscc metrics for clusters.
write_noise_model Estimates noise in single cell data.