Module `kitchen.kitchen`

Manipulate .h5ad files and cook scRNA-seq data from command line

Functions

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 cnmf_markers(args): Plots heatmap/matrix/dotplot of cNMF loadings for desired groups
def concatenate(args): Concatenates list of anndata objects in .h5ad format, keeping union of genes
def de(args): Performs differential expression analysis on a processed .h5ad file and plots results
def emptydrops(args): Labels cells using "emptydrops" method from CellRanger 3.0
def h5ad_to_csv(args): Converts counts matrix from .h5ad to flat file (.txt, .csv)
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 label_info(args): Prints value counts for .obs labels to console
def main()
def mtx_to_h5ad(args): Converts .mtx files from 10x CellRanger or DropEst to .h5ad
def obs_to_categorical(args): Makes .obs label categorical dtype
def pie(args): Plots populational pie charts for desired groups
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_X(args): Swaps a matrix from .layers to .X slot of anndata object, overwrites .h5ad file
def to_dense(args): Converts .X slot of anndata object to numpy.matrix format, overwrites .h5ad file
def to_h5ad(args): Converts counts matrix from flat file (.txt, .csv) to .h5ad
def to_sparse(args): Converts .X slot of anndata object to scipy CSR format, overwrites .h5ad file
def transpose(args): Transposes anndata object, replacing obs with var, and overwrites .h5ad file