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Applying XClone to mouse scRNA-seq: xcltk pre-processing for BAF data

2

To prepare scRNA-seq data for BAF analysis, xcltk is used. However, xcltk current does not support mm10 mouse scRNA-seq data at the baf_pre_phase.sh step, as it only permits usage of...

NickolasTeo

Applying XClone to mouse scRNA-seq: xclone.pp.xclonedata

3

xclone.pp.xclonedata currently only supports hg38 and hg19. Can you please also support mm10 for the RDR analysis of mouse scRNA-seq

NickolasTeo

RDR preprocessing filtering out all genes

1

Hello, I'm running into an issue with run_RDR where it filters out all genes. It looks like the minimum gene of 3000 is not being enforced? Thanks, Chang

cnk113

ref BAF strategy explore

1

- use variance to help keep ref BAF or not - may help to denoise some chrs

Rongtingting

[try to support 3.7, 3.8, 3.9 ](https://github.com/single-cell-genetics/XClone/issues/5#issuecomment-1520168936)

Rongtingting

RDR: libratio fitting bias

3

# Bad libraty ratio fitting raise Nan emm_prob_log ``` GX109_5400 dataset xconfig = xclone.XCloneConfig(dataset_name = dataset_name, module = "RDR") xconfig.set_figure_params(xclone= True, fontsize = 18) xconfig.outdir = out_dir xconfig.cell_anno_key = "cell_type"...

Rongtingting