Package `kitchen`

Manipulate counts matrix files and cook scRNA-seq data from command line

Sub-modules

kitchen.ingredients: Resources and utility functions
kitchen.kitchen: Manipulate .h5ad files and cook scRNA-seq data from command line
kitchen.plotting: Custom plotting functions for data in pd.DataFrame, anndata.AnnData, and decoupler formats
kitchen.recipes: Functions for processing and manipulating .h5ad objects and automated processing of scRNA-seq data

def add_label(args): Uses .obs_names from filtered counts matrix to add binary label to a reference anndata object, "True" = present in filt, "False" = not present. Overwrites reference .h5ad file.
def concatenate(args): Concatenates list of anndata objects in .h5ad format, keeping union of genes
def info(args): Prints information about .h5ad file to console
def knee_point(args): Labels cells using "knee point" method from CellRanger 2.1
def recipe(args): Full automated processing of scRNA-seq data
def rename_obs(args): Renames .obs columns in anndata object, and overwrites .h5ad file
def subset(args): Subsets anndata object on binary .obs label(s), saves to new .h5ad file
def to_h5ad(args): Converts counts matrix from flat file (.txt, .csv) to .h5ad
def transpose(args): Transposes anndata object, replacing obs with var, and overwrites .h5ad file