Man pages for diem
Debris-Containing Droplet Identification using EM

barcode_rank_plotCreate a barcode rank plot
call_targetsCall clean droplets after running EM
convert_to_seuratConvert an SCE object to Seurat
create_SCECreate an SCE object from a sparse matrix
diemRun DIEM pipeline
divide_by_colsumDivide elements of a column by the column's sum in a sparse...
dmmnCompute density of multinomial mixture for a matrix
dmultinom_sparseGet log multinomial density of columns in a sparse matrix.
droplet_dataReturn the droplet data from an SCE object
emEM function
e_step_mnComputed expected log likelihood of multinomial mixture
fill_countsFill information from raw counts
filter_genesFilter out lowly expressed genes
fraction_logfraction of logs
gene_dataReturn the gene data from an SCE object
get_clean_idsReturn IDs of clean droplets
get_gene_pctGet percent of reads align to given gene(s)
get_knnGet k-nearest neighbor graph
get_removed_idsReturn IDs of removed droplets
get_var_genesGet variable genes
initialize_clustersInitialize clustering for EM
init_paramInitialize EM parameters given group assignments
mb_smallSingle-nucleus RNA-seq of mouse brain
m_step_mnMaximize multinomial parameters in EM
normalize_dataNormalize raw counts.
norm_countsNormalize counts of a sparse matrix
plot_umi_geneScatterplot of genes vs. UMI counts, colored by posterior...
plot_umi_gene_callScatterplot of genes vs. UMI counts, colored by call
raw_countsReturn raw counts
read_10xRead 10X counts data
run_emRun EM on counts to estimate multinomial mixture model
set_cluster_setSet droplets for cluster initialization
set_debris_test_setSet debris and test droplets
sum_logsum of logs
diem documentation built on Nov. 16, 2019, 1:08 a.m.