User: from the mountains
from the mountains • 80
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Posts by from the mountains
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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 mountains • 80
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1
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... 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 mountains • 80
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... i guess my question is, will merge do any normalization or removal of batch effects? ...
written 8 weeks ago by
from the mountains • 80
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... 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 mountains • 80
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... 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 ...
written 8 weeks ago by
from the mountains • 80
• updated
8 weeks ago by
jared.andrews07 • 3.8k
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... `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 mountains • 80
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3
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... 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 mountains • 80
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2
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... try option -v 4 to get better debugging output. ...
written 3 months ago by
from the mountains • 80
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... 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 mountains • 80
2
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0
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382
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... 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 ...
written 12 months ago by
from the mountains • 80
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