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

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Documentation for package ‘BEARscc’ version 1.22.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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.