Man pages for vallotlab/IDclust
Iterative Differential Clustering for single-cell

add_gene_to_DA_listAdd genes to differential analysis using a...
calculate_FalseNegativeCalculate False Negative markers for SingleCellExperiment...
calculate_FalsePositiveCalculate False Positives markers for SingleCellExperiment...
create_pseudobulk_matCreate Pseudo-Bulk Matrice from scRNA clusters & replicates
create_pseudobulk_mat.defaultCreate Pseudo-Bulk Matrix from scEpigenomics clusters &...
create_pseudobulk_mat.SeuratCreate Pseudo-Bulk Matrice from scRNA clusters & replicates
differential_ChromSCapeDifferential analysis with ChromSCape (differential...
differential_edgeR_pseudobulk_LRTPseudo-bulk differential analysis with edgeR (LRT)
differential_edgeR_pseudobulk_LRT.defaultPseudo-bulk differential analysis with edgeR (LRT)
differential_edgeR_pseudobulk_LRT.SeuratPseudo-bulk differential analysis with edgeR (LRT)
differential_pathwayFind differential pathways with enrichR
differential_SeuratDifferential function Seurat (wilcoxon)
find_differentiated_clustersFind Differentiated Clusters
IDC_DA_scEpigenomicsA data.frame containing the differential markers for...
IDC_DA_scRNAA data.frame containing the differential markers for scRNA...
IDC_summary_scEpigenomicsA data.frame containing the summary of differential markers...
IDC_summary_scRNAA data.frame containing the summary of differential markers...
iterative_differential_clusteringiterative_differential_clustering
lm_listA list of linear models of false positive differential...
plot_cluster_networkPlot Iterative Differential Clustering network
processing_ChromSCapeNormalize and run PCA with ChromSCape (LSI)
processing_SeuratNormalize and run PCA with Seurat
scExpA SingleCellExperiment object containing the scH3K27ac part...
SeuA Seurat object containing the scRNA part of Paired-Tag...
summarise_DASummarise Differential Analysis table
top_differential_markersRetrieve top marker genes from list of differential analysis
top_enriched_pathwaysFind enriched pathways in marker genes of IDclust
vallotlab/IDclust documentation built on July 5, 2024, 3:26 p.m.