Parquet format

[megleila]

Hello -- I am having an issue reading in the data because my Xenium output data are in the newer version of output files, parquet files rather than .csv.gz files (e.g. transcripts.csv.gz is now transcripts.parquet). Is there a workaround for this or update to CellScopes?

[HaojiaWu]

Hi @megleila
Yes, this is fixed in the dev version of the package. Please upgrade your Julia to version 1.10.4 and install the development branch like this (assuming that you are using linux server).
In Terminal:

wget https://julialang-s3.julialang.org/bin/linux/x64/1.10/julia-1.10.4-linux-x86_64.tar.gz
tar xvf julia-1.10.4-linux-x86_64.tar.gz
# export julia to your path

In Julia:

using Pkg
Pkg.add(PackageSpec(url="https://github.com/bicycle1885/Leiden.jl"))
Pkg.add(PackageSpec(url="https://github.com/HaojiaWu/CellScopes.jl", rev="dev"))