Table 1 Main tasks and corresponding functions in scMuffin

Create the scMuffinList

Create the scMuffinList from counts and normalized expression data

create_scMuffinList()

Add a partition

Add a partition of cell (clusters)

add_partition()

Gene set expression scoring

Average gene set expression deviation from matched empirical reference

Provided gene sets from CellMarker [12], PanglaoDB [13], CancerSEA [14] and MSigDB [8]

prepare_gsls()

calculate_gs_scores()

calculate_gs_scores_in_clusters()

CNV

Estimation of CNVs by means of the “moving window” approach, that is, considering the expression of adjacent genes

Calculation of CNV deviation from a normal reference profile

Processing of normal tissue-specific expression data from GTEx

Detection of CNV regions

CNV_analysis()

process_GTEx_gene_reads()

Transcriptional complexity

Number of expressed genes in relation to the total reads, calculated using a ratio, linear model residuals and entropy

transcr_compl()

Proliferation

Maximum between G1/S and G2/M gene set scores

proliferation_analysis()

Cell state trajectory

Diffusion map computation

diff_map()

Cell cluster annotation

Assessment of cluster enrichment for quantitative and categorical features

assess_cluster_enrichment()

Comparison of datasets

Assessment of cluster markers or gene set expression across multiple datasets

inter_dataset_comparison()

Visualization

Automated UMAP visualizations for multiple features

Heatmaps: gene set scores, CNV, overlap between clusters

Boxplots and barplots of cluster enrichment

Diffusion maps

boxplot_cluster()

dotplot_cluster()

heatmap_CNV()

plot_profile_CNV()

plot_umap_colored_features()

plot_heatmap_features_by_clusters()

plot_diff_map()