Seurat3-plus

A set of R codes to make Seurat3 running easier

Import/Export/File format conversion:

ImportMetadata and ImportMetadataCSV plugs in the metadata information stored in a data.frame or csv file into an existing Seurat object.

SaveUMAP saves a specified embedding(such as UMAP)'s coordinates into a csv file.

Meta2UMAP converts the embedding coordinates that were saved in the as metadata in the Seurat object into the embedding slots.

MM10X_to_Seurat reads data in MatrixMarket format (with metadata stored in "metadata.tsv") into a Seurat object,.

Seurat_to_MM10X writes the Seurat object's counts and meta.data into MatrixMarket and tsv files.

Other functions:

DefaultRun quickly runs a Seurat workflow to process a Seurat object (Normalize, HVG, regress, scale, PCA, cluster, tSNE). It is useful to quickly fill the slots of a Seurat object with placeholders.

PairwiseMarkers compares every pair of two cell types and returns marker genes.

JackstrawSummary reports the significant (useful) PCs after Jackstraw algorithm to filter out the significant PCs.