biomystery snATAC_pipeline_scanpy_based issues - Githubissues

biomystery / snATAC_pipeline_scanpy_based

A single-cell ATAC pipeline based on scanpy and clustering on most variable genomic bins. Originated from Josh@Kyle's lab.

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round 2 clustering on base of peaks

#10 biomystery opened 4 years ago
1
promoter - cell matrix calculation

#9 biomystery opened 4 years ago
0
bugs in save h5ad in NAS

#8 biomystery opened 4 years ago
0
doublet removal

#7 biomystery opened 5 years ago
1
integrate cecero calculation

#6 biomystery opened 5 years ago
1
integrate chromVar calculation

#5 biomystery opened 5 years ago
0
add TSS score calculation in preprocess

#4 biomystery opened 5 years ago
2
auto detect threshold by finds number of guassian automatically

#3 biomystery closed 4 years ago
0
Optimal - make parallel at reads handling steps (shift, dedup, added barcodes)

#2 biomystery opened 5 years ago
0
Replace `samtools` sort to faster `sambama` sort

#1 biomystery opened 5 years ago
0