Function reference • scMuffin

All functions

CNV(): CNV

CNV_analysis(): CNV analysis

add_features(): Add a feature to scMuffinList

add_partitions(): Adds a clustering to the clustering list

adj_outliers_col(): Remove outliers to avoid that these influence colors

apply_CNV_reference(): apply_CNV_reference

assess_cluster_enrichment(): Assess enrichment with ORA or CSEA

barplot_cluster(): Barplot of cluster enrichment in a categorical feature

boxplot_cluster(): Boxplot of cluster enrichment in a quantitative feature

boxplot_points(): Boxplot with points

calc_gs_perm(): Calculate permutations

calculate_CNV(): Calculate CNV

calculate_gs_scores(): Calculate gene set scores

calculate_gs_scores_in_clusters(): Calculate gene set score at cluster level

cel_coocc_partitions(): Co-occurrence of cells between two partitions

cluster_by_features(): Cluster by features

cluster_csea(): Calculate cluster enrichment by means of CSEA

cluster_hyper(): Calculate cluster enrichment by hypergeometric test

cluster_stats(): Cell cluster statistics

create_scMuffinList(): Create scMuffinList

csea(): Gene Set Enrichment Analysis

detect_CNV_regions(): Detect CNV regions

diff_map(): Computation of Diffusion Map and Diffusion Pseudo Time

es(): Enrichment Score

extract_cluster_enrichment_table(): Extract cluster enrichment table

extract_cluster_enrichment_tags(): Extract the top results of CSEA and ORA for each cluster

genes_in_detected_CNV_regions(): Retrieve genes in detected CNV regions

get_msigdb_geneset(): Returns msigdb geneset in a format compatible with calculate_signatures()

gs_score(): Gene set scoring

gs_scores_in_clusters(): Gene set scoring at cluster level

gsls_EntrezID: Gene set lists (Entrez Gene ID) Gene set lists collected from the following sources: - CancerSEA: http://biocc.hrbmu.edu.cn/CancerSEA/goDownload - CM_cancer: http://bio-bigdata.hrbmu.edu.cn/CellMarker - CM_normal: http://bio-bigdata.hrbmu.edu.cn/CellMarker - PNDB: https://panglaodb.se - Tirosh2016: 10.1126/science.aad0501 - Ribosomal proteins:

gsls_Symbol: Gene set lists (Symbol) Gene set lists collected from the following sources: - CancerSEA: http://biocc.hrbmu.edu.cn/CancerSEA/goDownload - CM_cancer: http://bio-bigdata.hrbmu.edu.cn/CellMarker - CM_normal: http://bio-bigdata.hrbmu.edu.cn/CellMarker - PNDB: https://panglaodb.se - Tirosh2016: 10.1126/science.aad0501 - Ribosomal proteins:

heatmap_CNV(): CNV Heatmap

inter_dataset_comparison(): Inter-dataset cluster similarity

keep_strongest_representative(): Keep the feature with the highest average across cells

ora(): Over Representation Analysis

ora1gs(): Hypergeometric test on 1 feature set

overlap_coefficient(): Calculate the overlap coefficient between two sets

overlap_matrix(): Calculate the overlap matrix between clusters

partitions_to_list(): Transform partitions to lists

plot_diff_map(): Plot diffusion map colored by other features

plot_heatmap_dataset_comparison(): plot_heatmap_dataset_comparison

plot_heatmap_features_by_clusters(): Plot an heatmap of feature values in cell clusters

plot_profile_CNV(): CNV Profile

plot_umap(): plot_umap

plot_umap_colored_features(): UMAP Visualization colored by features

prepare_cluster_markers_list(): Prepare cluster markers list Prepare cluster markers list for inter_dataset_comparison

prepare_gsls(): Prepare the gene set lists collected from various sources

preprocess_for_heatmap_CNV(): preprocess_for_heatmap_CNV

preprocess_object_for_CNV(): preprocess_object_for_CNV

process_GTEx_gene_reads(): Process GTEx expression data

proliferation_analysis(): Define a proliferation score

regions_to_genes(): Create a map between CNV regions and genes

scML_demo: scML_demo scMuffinList object with a partial dataset used in vignettes.

sc_create_null(): Create empirical null for gene set scoring

sc_data_bin(): Split the genes into bins by their expression

show_tissues(): Show the tissues available for prepare_gsls

transcr_compl(): Transcriptional Complexity and Entropy