User: yzhao140

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yzhao1400
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Posts by yzhao140

<prev • 15 results • page 1 of 2 • next >
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Comment: C: Annotate PBMC scRNA-seq data
... So what can I do if I only want to use scRNA-seq data to do annotations? ...
written 24 days ago by yzhao1400
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Comment: C: Annotate PBMC scRNA-seq data
... Thank you very much! I will have a try. ...
written 5 weeks ago by yzhao1400
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Annotate PBMC scRNA-seq data
... Hi, all! I am dealing with this dataset https://support.10xgenomics.com/single-cell-multiome-atac-gex/datasets/1.0.0/pbmc_granulocyte_sorted_3k. I need to identify the cell type for each cell then do unpervised clustering etc. Do you have any suggestions? ...
rna-seq written 5 weeks ago by yzhao1400 • updated 5 weeks ago by igor12k
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10X Genomics, Single Cell Multiome ATAC-seq and RNA-seq data
... Hi, all! I did a project using this dataset https://support.10xgenomics.com/single-cell-multiome-atac-gex/datasets/1.0.0/human_brain_3k. You can download the data using this link https://cf.10xgenomics.com/samples/cell-arc/1.0.0/human_brain_3k/human_brain_3k_filtered_feature_bc_matrix.tar.gz. But wh ...
atac-seq written 5 weeks ago by yzhao1400
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Comment: C: Loading Matrices of 10X Genomics failed
... Thank you for your remind. I solved it by csv.reader(codecs.iterdecode(gzip.open(features_path), 'utf-8') ...
written 5 weeks ago by yzhao1400
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Loading Matrices of 10X Genomics failed
... I am loading Matrices of 10X genomics Single Cell Multiome ATAC+ Gene Exp's output into Python. I just go through the instruction of 10X genomics. (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/output/matrices?src=social&lss=facebook&cnm=soc-fb-ra_g- ...
software error rna-seq written 7 weeks ago by yzhao1400 • updated 7 weeks ago by karl.stamm3.9k
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Comment: C: Extracting count matrix from default cell ranger files
... Is this workflow correct? https://cf.10xgenomics.com/supp/cell-exp/notebook_tutorial-3.0.0.html ...
written 7 weeks ago by yzhao1400
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Comment: C: Extracting count matrix from default cell ranger files
... I am on mac. But https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/h5_matrices relies on software "Cell Ranger" which can not be installed in a laptop? ...
written 7 weeks ago by yzhao1400
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Comment: C: Extracting count matrix from default cell ranger files
... Thank you very much! I also have a small question. Is there a way for me to finish the task in laptop via Python. It seems that https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/h5_matrices should be done in linux system? ...
written 7 weeks ago by yzhao1400
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Comment: C: Extracting count matrix from default cell ranger files
... Sorry, there may be a typo here for "non programmatic". I want to get a gene by cell count matrix and use it as input for a model in python. ...
written 8 weeks ago by yzhao1400

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