User: leranwangcs
leranwangcs • 40
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- 6 days, 16 hours ago
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Posts by leranwangcs
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... Thanks, but it doesn't seem to be the solution.... After digging into varies forums, the only way for me to go seemly is to update my mac version, then install R 4.0, then install the higher version of AnnotationHub which has fixed the bugs. I obviously don't want to update my mac version... ...
written 6 days ago by
leranwangcs • 40
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... Thanks, but it doesn't seem to be the solution.... After digging into varies forums, the only way for me to go seemly is to update my mac version, then install R 4.0, then install the higher version of AnnotationHub which has fixed the bugs. I obviously don't want to update my mac version... ...
written 6 days ago by
leranwangcs • 40
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... Hi,
I'm trying to use SingleR to annotate my Seurat object, but the ImmGenData() keeps throwing me errors:
Error in UseMethod("filter_") :
no applicable method for 'filter_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
Based on some ...
written 8 days ago by
leranwangcs • 40
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... Thanks very much for your help!! ...
written 8 days ago by
leranwangcs • 40
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... Thanks for the reply! I was confused because in a seurat tutorial, it says there was a column called cellType which looks like this:
## nGene nUMI orig.ident celltypes nCount_RNA nFeature_RNA
## X7873M.1 3563 11796 SeuratProject Macrophage 11796 3563
## X ...
written 10 days ago by
leranwangcs • 40
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... Hi,
I'm trying to extract cell names from my seurat object. I tried
colnames(BAAK_B@assays$RNA@data)
But all I got was:
"AATGAAGAGAGCCGTA-1" "ACTATGGGTTGACGGA-1" "ACTGTCCAGGAAGTCC-1" "AGATCGTCACTTGTCC-1" "AGCGTATAGTCTTGGT-1" "AGCGTATCACTCTAGA-1" "AGCTACAGTCCAGCAC-1" "AGCTTCCGTGGCAGAT-1" ...
written 10 days ago by
leranwangcs • 40
• updated
10 days ago by
from the mountains • 130
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... To answer myself's question: I used a vdj database for my gene expression data. So when I switch to the correct databases, it worked. ...
written 6 weeks ago by
leranwangcs • 40
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... Yeah I should have, Sorry about that! Here is my command:
cellranger count --id=run_count_BAAK-FCW-FW099J --transcriptome=/scratch/mtblab/leran/scRNA_seq/ref/refdata-cellranger-vdj-GRCm38-alts-ensembl-5.0.0 --fastqs=/scratch/mtblab/leran/scRNA_seq/data --sample=BAAK-FCW-FW099J-1A-1,BAAK-FCW-FW0 ...
written 7 weeks ago by
leranwangcs • 40
• updated
7 weeks ago by
rpolicastro ♦ 4.0k
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... I downloaded the cell ranger reference database from
wget https://cf.10xgenomics.com/supp/cell-vdj/refdata-cellranger-vdj-GRCm38-alts-ensembl-5.0.0.tar.gz
then I tar tar xvzf the .tar.gz file and got a refdata-cellranger-vdj-GRCm38-alts-ensembl-5.0.0 folder in my path.
But when I run the cell range ...
written 7 weeks ago by
leranwangcs • 40
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