Gert Hulselmans
Gert Hulselmans
Read the docs page is updated with lastest pySCENIC and Feather v2 database file names.
pySCENIC v0.12.0 is out, which uses Feather v2 database files. https://pypi.org/project/pyscenic/
`num_workers` is the number of threads that are spawned.
Install pySCENIC 0.12.0: https://pypi.org/project/pyscenic/
> > Install pySCENIC 0.12.0: https://pypi.org/project/pyscenic/ > > pretty sure"mm9.feather" it's the problem. I used "mm10_10kbp_up_10kbp_down_full_tx_clustered.genes_vs_motifs.rankings.feather" & "mm10_500bp_up_100bp_down_full_tx_clustered.genes_vs_motifs.rankings.feather" run perfectly find! Now the only question is, if I use the...
@xAZx I might have a solution for your problem. In my case `dsc-pileup` was very slow (took for some test samples 200 hours). So I made the following: https://github.com/aertslab/popscle_helper_tools which...
Try filtering the BAM file first so only the reads that have SNPs and are in the cell barcode file are retained: https://github.com/aertslab/popscle_helper_tools/#filter-bam-file-for-usage-with-popscle-dsc-pileup Depending on the VCF file, this can...
@allumette Check https://github.com/statgen/popscle/issues/22, it might help for your case too. I designed it for speeding up `dsc-pileup` but it might have a much lower memory usage too.
This will work in the next Polars release. Random python object support is improved in: https://github.com/pola-rs/polars/pull/5275 ```python In [3]: ...: ...: class silly(): ...: def __init__(self,junk: str): ...: self.junk =...
Looking at it now.