User: rmf
rmf • 970
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Posts by rmf
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... BUSCO is what I use at the moment and was wondering if there was something better. Something like AED scores. Thanks for BEACON. Never heard of that. ...
written 4 weeks ago by
rmf • 970
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... If I have multiple annotations (gff/gtf files) for a genome, are there tools/metrics to evaluate which annotation is better? ...
written 4 weeks ago by
rmf • 970
• updated
4 weeks ago by
hugo.avila • 110
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Comment:
C: RNA velocity plot demystified
... Thanks for that. That might be helpful even though I don't understand python code. And the R notebooks unfortunately don't seem to go into so much detail. Anyhow, my question still stands as to what the LENGTH of the arrows mean. ...
written 7 months ago by
rmf • 970
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... Here is an example of RNA velocity from [Manno .et .al 2018](https://www.nature.com/articles/s41586-018-0414-6).
![enter image description here][1]
Colour of cells denote cell type. Layout denotes how cells cluster by some measure of similarity. The direction of the arrows denote the future state ...
written 7 months ago by
rmf • 970
• updated
7 months ago by
dchatterjee • 30
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... I am trying to move data from Seurat to ScanPy. It seems like exporting to loom is one of the ways to do it.
In R, I am using an example dataset.
library(Seurat)
library(loomR)
lfile <- as.loom(x=pbmc_small,filename="python/pbmc.loom")
lfile$close_all()
In python, I read it in ...
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... I have PacBio reads from three bacterial genomes as three samples. They were de-novo assembled using HGAP4 and polished. One of samples was taken as reference. And subreads from each sample was mapped back to this reference for variant calling. Variant calling was performed using two workflows:
...
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... I have some pacbio reads. That's really the only info I have. No version number or anything. Each sample has four bax.h5 and one bas.h5. Is it possible to convert this to consensus reads?
I tried running the `css` tool from `pbcss`. It runs but I get the report below:
ZMW Yield
Success (wi ...
written 13 months ago by
rmf • 970
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... I also had the feeling something is wrong. Then, I have looked into it and I don't see anything obviously wrong. So, in the first plot, I use *nFeatures_RNA*, In the second plot, I manually recalculate *num of genes detected* from 'integrated' assay using `colSums(GetAssayData(su,assay="integrated") ...
written 14 months ago by
rmf • 970
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... I have three 10X runs. If I merge them with `CreateSeuratObject()`, this is the distribution of genes detected for each run (batch) (nFeatures_RNA).
![enter image description here][1]
If I integrate them, using hvg approach or sctransform approach. (Showing sctransform based integration below)
...
written 14 months ago by
rmf • 970
4
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2.6k
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... tSNE separates groups quite well, but does not preserve the global structure very well, therefore you cannot take three points and say two are closer than the other two. It does not preserve distance. Local structures may make sense. Therefore, it most likely doesn't show cell differentiation trajec ...
written 16 months ago by
rmf • 970
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