Missing data about hgg-oncohistones HOT 4 CLOSED

Hi Yile,

The integration script for harmony is at code/scripts/integrate_harmony.R.
I've added some more details in this section: https://github.com/fungenomics/HGG-oncohistones/blob/master/README.md#data-integration

Selin

from hgg-oncohistones.

Hi, thanks for the kind words and for checking out the code!

Thanks for catching that. The first file you mentioned was located outside this directory, but I have added a copy to this repo. You can now find the folder which is referenced as SEURAT_V3_ASSETS or file.path(params$assets, "resources") in the various preprocessing_*.Rmd scripts here: https://github.com/fungenomics/HGG-oncohistones/tree/master/code/seurat_v3_resources, and that contains CellCycleGeneList_1134_whitfield_2002_mice_gene_symbols.txt.

For the second, the script to produce that file is here: https://github.com/fungenomics/HGG-oncohistones/blob/master/code/scripts/make_scATAC_refs.R. It essentially follows directions in the Signac package.

Selin

from hgg-oncohistones.

Hi Selin,

Really thanks for the reply and for sharing the code and the data.
I also would like to know how you integrated multiuome data (RNA + ATAC) across samples. I didn't find the related codes.
Could you also share it?
If I missed it, could you tell me where I can find it in this repo?
Thanks!

Best,
Yile

from hgg-oncohistones.

Hi Selin,

Thanks a lot! I will have a look.

Yile

from hgg-oncohistones.