Gert Hulselmans

Does the /data directory contain the mentioned files?

If BEDtools would use HTSlib, it would get this support for free: http://www.htslib.org/ header file: *htslib/faidx.h* HTSlib could be useful for general VCF/BCF/SAM/BAM/CRAM, gzipped input files indexed by bgzip, reading...

Good news for you all. I finally had some time to rewrite the old code and it is a lot more efficient and would be able to run even on...

You can find it now in the `polars_1xx` branch: https://github.com/aertslab/pycisTopic/commit/2fa44648cf5a264e4b46da47c3c918975a9e68b2#diff-b1472e8f1bcc609e65e2db670ba21144389567776cf0a1089ecf4e0c5749fa22R1024-R1050

@JinKyu-Cheong @yojetsharma Running `impute_accessibility` and `normalize_scores` is now not necessary anymore. See: https://github.com/aertslab/pycisTopic/issues/195#issuecomment-2528381878 for instructions.

With the Polars 1xx branch it is now possible to make a Mallet corpus file from a binary count matrix file in Matrix Market format: ```python Expose creation of Mallet...

It might be an interesting test to see if more recent versions of `AnnData` fix this memory issue (as there seem to be some sparse matrix fixes). What type does...

seems like it is not using a sparse matrix.

It might choke on: ```python timepoint: Int64 ``` https://pandas.pydata.org/docs/reference/api/pandas.arrays.IntegerArray.html#pandas.arrays.IntegerArray https://pandas.pydata.org/docs/user_guide/integer_na.html#integer-na I am not a Pandas user, but as far as I know `IntX` (with capital `I`) is a new Pandas...

Probably downgrading Pandas to `1.5.3 (