Main fixsnakemake - #17

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Congm12 wants to merge 11 commits into

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main_fixsnakemake

Commits on Dec 2, 2024

handle the non-gzipped barcodes in preprocessing
Cong Ma
committed
af8f384
update readme
Cong Ma
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930ca4f

Commits on Dec 8, 2024

preprocessing step get_snp_matrix.py keep sparse matrix operation to save mem
Cong Ma
committed
6ff2d37

Commits on Dec 10, 2024

sparse matrix operations for allele counts and transcript counts, sparse intermediate count matrices for haplotype blocks, pd dataframe operations to vectors
Cong Ma
committed
e5cdda0
add min UMI threshold for constructing haplotype blocks
Cong Ma
committed
6d38526

Commits on Dec 12, 2024

output more intermediate files in parsing inputs
Cong Ma
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465c351

Commits on Dec 13, 2024

allow reading other modalities in read_10x_h5
Cong Ma
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61d6e17
sub-sample spots and snps
Cong Ma
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6a4b696

Commits on Jan 11, 2025

add a separate wrapper for plot spatial clones that takes figsize and point size as input
Cong Ma
committed
0fae234

Commits on Apr 17, 2025