User: leranwangcs

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leranwangcs40
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Posts by leranwangcs

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Kept getting issue when using ImmGenData() in SingleR
... 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 leranwangcs40
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Answer: A: Kept getting issue when using ImmGenData() in SingleR
... 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 leranwangcs40
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Kept getting issue when using ImmGenData() in SingleR
... 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 ...
R singler written 8 days ago by leranwangcs40
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Comment: C: How to get real cell names from Seurat Object?
... Thanks very much for your help!! ...
written 8 days ago by leranwangcs40
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Comment: C: How to get real cell names from Seurat Object?
... 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 leranwangcs40
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How to get real cell names from Seurat Object?
... 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" ...
rna-seq written 10 days ago by leranwangcs40 • updated 10 days ago by from the mountains130
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Answer: A: cellranger count error "Your reference does not contain the expected files, or t
... 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 leranwangcs40
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Comment: C: cellranger count error "Your reference does not contain the expected files, or t
... 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 leranwangcs40 • updated 7 weeks ago by rpolicastro4.0k
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cellranger count error "Your reference does not contain the expected files, or they are not readable. Please check your reference folder on n145"
... 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 ...
rna-seq written 7 weeks ago by leranwangcs40

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