Yuanjian Huang

hello @elfofmaxwell, thanks for the response. I think the documents for `dynamo.pl.scatters()` is wrong. It mentions `If “both”, it will save and plot the figure at the same time. If...

Hello @Xiaojieqiu Thanks for the response. The tutorial did as below ```python adata = dyn.sample_data.hematopoiesis() adata AnnData object with n_obs × n_vars = 1947 × 1956 obs: 'batch', 'time', 'cell_type',...

Thanks @Xiaojieqiu. If I didn't misunderstand, I think this code line is missing in the tutorial. That's why it made me confused. Thanks for the response!

Hello @Xiaojieqiu Could you please tell me how you get the table showing `Bas_Ery_curv`?  I can only get the table like below. Note that the first row has nothing...

in my case, ```r BiocManager::install("BioinformaticsFMRP/TCGAbiolinksGUI.data") BiocManager::install("ExperimentHub") ``` Restart R ```r BiocManager::install("BioinformaticsFMRP/TCGAbiolinks") ``` works

Hello @cflerin BUG report, may be caused by Dask. `pyscenic grn {EXP_MTX_QC_FNAME} {HUMAN_TFS_FNAME} -o {ADJACENCIES_FNAME} --num_workers 16` only works at `--num_workers 16`. If `num_workers` is more than 16, whatever the...

I think the distribution of the color bar is determined by the cell order in the auc_mtx and bin_mtx. So I sorted the auc_mtx and bin_mtx by the leiden cell...

I have the same question! The authors did no normalization (`sc.pp.normalize_total()` and `sc.pp.log1p()`) before proceeding to the GRNBoost2 step in the PBMC tutorial (https://github.com/aertslab/SCENICprotocol/blob/master/notebooks/PBMC10k_SCENIC-protocol-CLI.ipynb), but they did `sc.pp.log1p()` for the...

Hello @taoliu, just want to check whether it is available to call HMMRATAC in MACS3 now? I didn't find this sub function in MACS3.  Thanks! Best, YJ

run this ```python conda install numpy scipy cython numba matplotlib scikit-learn h5py click pip install -U pysam loompy sudo apt update sudo apt install build-essential pip install velocyto ```