Quang Nguyen

Error in run10X: logging.debug(f"Example of barcode: {valid_bcs_list[0].split('-')[0]} and cell_id: {valid_cellid_list[0]}") - IndexError: list index out of range

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Hi there, I was running `velocyto run10x -m /ceph/project/....../mm10_rmsk_chrMTGTF.gtf /ceph/project/........../10x_scRNA_704-187_CD8P_GEX /ceph/project/borrowlab/shared/scRNASeq_blood_220210/xenon/Blood_CD8T_TranscriptomeTCRseq/Blood_CD8T_scTranscriptome/run_cellranger_count_chrMTGTF/refdata-gex-GRCh38-2020-A_chrMTGTF/genes/genes.gtf` The `/ceph/project/........../10x_scRNA_704-187_CD8P_GEX` points to the folder `10x_scRNA_704-187_CD8P_GEX` that contains my `outs` folder, which contains the `possorted_genome_bam.bam` that I had...

tidyseurat::aggregate_cells doesn't pull all meta.data columns of Seurat object?

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Hi there, Thanks for a great tool. `tidyseurat::aggregate_cells` only pull some but not all metadata columns of the original Seurat object. Would you mind taking a look? Thank you again....

Hi @zhanghao-njmu, Thank you for the package! Related to #109, I hope to get some clarification regarding the input data. I had loom objects for different samples generated by `velocyto`,...

ValueError: '_index' is a reserved name for dataframe columns. Above error raised while writing key 'var' of to /

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Hi there, I was trying to write my adata with `write_h5ad` which has my loom objects merged with my Seurat object in Python so that I can then convert it...

Hi there, Thanks for the tool! I wondered why the plots at https://zhanghao-njmu.github.io/SCP/ are all corrupted? Does the tutorials at https://zhanghao-njmu.github.io/SCP/ the same as the one on this GitHub page?...

Hi, Helena, Thank you for the package. I ran `sce$i

Hi there, Thanks for the tool. The markers listed for the `celltype.l2` at https://azimuth.hubmapconsortium.org/references/#Human%20-%20Tonsil for the human tonsil reference dataset are not correct and are entirely different from what detailed...

Error during installation of azimuth package due to "dependency ‘presto’ is not available for package ‘Azimuth’"

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Hi there, I attempted to `devtools::install_github("satijalab/azimuth")` but encountered the `ERROR: dependency ‘presto’ is not available for package ‘Azimuth’` as below (reported also in https://github.com/immunogenomics/presto/issues/16) Would you mind helping me to...

Clarifications about `.abundance_counts`

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Hi @stemangiola - My apologies for re-asking these questions following up from #92. Would you mind giving me some pointers? Q1. Would you mind confirming that the duplicated cell identifiers...

Advice for automated cell classification workflow between datasets with different number of parameters

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Hi there, Thanks again for the tool. I have 1 FCS that was acquired by the Aurora and 1 FCS that was acquired by Fortessa with much less number of...