User: from the mountains

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Posts by from the mountains

<prev • 52 results • page 1 of 6 • next >
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Answer: A: fastest UMAP method
... I am using `sample <- RunUMAP(sample, umap.method = "umap-learn")` which might require installation of umap-learn and some dependencies in Python. ...
written 14 days ago by from the mountains80
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Comment: C: Seurat integrated analysis with replicates
... got it, i think i didn't see your edit after you initially answered the question. Thank you. ...
written 5 weeks ago by from the mountains80
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Comment: C: Seurat integrated analysis with replicates
... i guess my question is, will merge do any normalization or removal of batch effects? ...
written 8 weeks ago by from the mountains80
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Comment: C: Seurat integrated analysis with replicates
... Thank you for taking the time to answer my question. But then what is the purpose of Seurat's merge? ...
written 8 weeks ago by from the mountains80
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Seurat integrated analysis with replicates
... I have done some exploring with Seurat integrated analysis and was wondering how I can incorporate biological replicates. So in a hypothetical experimental design, I would have 2 biological replicates for untreated samples and 2 biological replicates (same platform for everything). How would I go ab ...
R single cell dropseq rna-seq written 8 weeks ago by from the mountains80 • updated 8 weeks ago by jared.andrews073.8k
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Comment: C: How to merge multiple single cell sequencing data after processing by CellRanger
... `cellranger aggr` merges together the data by normalization of reads mapped. running multi-sample CCA looks for correlation structures of gene-gene relationships and uses that to figure out how cells in one sample correlate best with those in another sample. I wouldn't say CCA is the same as a merge ...
written 8 weeks ago by from the mountains80
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Comment: C: How can I convert VCF to HGVS format?
... anyway to use hgvs on a custom reference? i want to get the hgvs representation convention, without relying on a public reference or external database. ...
written 10 weeks ago by from the mountains80
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Comment: A: bwa mem: fail to locate the index files
... try option -v 4 to get better debugging output. ...
written 3 months ago by from the mountains80
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Comment: C: How to change filtering parameters in gff3 -> gtf conversion using gffread?
... i'm not sure if this answers my question. The input examples i show are both transcript features and their gbkey is transcript as well. How come one is retained in output.gtf but the other isn't? ...
written 12 months ago by from the mountains80
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How to change filtering parameters in gff3 -> gtf conversion using gffread?
... I'm trying to convert a gff3 to gtf with gffread and i'm seeing unexpected filtering of most records in the gff3. it is for a viral genome. Only 10 out of 180 are going through. curiously, the first of these two records are converting, but the second is not: EF999921.1 Genbank transcript 60089 ...
software error data formatting written 12 months ago by from the mountains80

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