cellxmer

Convert a Malva Index into a cell-by-chunk AnnData object that can be used to cluster cells directly from sequence composition

usage: malva cellxmer [-h] [--index-in INDEX_IN] --h5ad-out H5AD_OUT [--save-kmer] [--kmer-min KMER_MIN] [--kmer-max KMER_MAX] [--bin-size BIN_SIZE] [--w-size W_SIZE] [--num-buckets NUM_BUCKETS]
                      [--chunk-size CHUNK_SIZE] [--tmp-dir TMP_DIR]

Named Arguments

--index-in

Valid directory where the malva index (and metadata) is located.

The directory must contain the file malva_index.h5. Otherwise, an exception will be thrown.

--h5ad-out

Directory where the cell-by-mer object will be stored.

--save-kmer

When specified, also saves the cell-by-kmer matrix together with the cell-by-bucket matrix

Default: False

--kmer-min

k-mers occurring less than –kmer-min times are ignored

Default: 10

--kmer-max

k-mers occurring more than –kmer-max times are ignored

Default: 10000

--bin-size

Aggregates spatial units at the final AnnData file to reduce dimensions of final cell-by-kmer matrix

Default: 0

--w-size

W-mer size for filtering (default: 16, must be <= k-mer size)

Default: 16

--num-buckets

Number of buckets for clustering k-mers (default: 100,000)

Default: 100000

--chunk-size

Number of k-mers to process in each chunk (default: 1,000,000)

Default: 1000000

--tmp-dir

Directory for temporary files (default: system temp directory)