User: rmf
rmf • 690
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Posts by rmf
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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 2 days ago by
rmf • 690
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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 3 days ago by
rmf • 690
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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 10 weeks ago by
rmf • 690
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... I use raw counts for DGE in DESeq2, edgeR etc. And I use VST for PCA and clustering.
Now, I am curious about TPM. What are the applications of a TPM normalised count table? What can it be used for? What are the drawbacks of TPM normalised counts?
![enter image description here][1]
![enter image de ...
written 10 weeks ago by
rmf • 690
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... I am using limma to test for differential expression. And I am trying to find the best model to use. My variable of interest is **condition**. I have several batch variables **plate**, **well** and **gender** which seems to be highly associated with top three principal components in a PCA.
I have f ...
written 3 months ago by
rmf • 690
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... This is the code that I use in R.
#' @title get_mv
#' @description Compute M values from beta values
#' @param B A beta value matrix where rows are probes and columns are samples
#' @return Returns an M value matrix
#'
get_mv <- function(B)
{
if(missing(B)) st ...
written 4 months ago by
rmf • 690
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... Once you figure out what the different parts of your header mean, you can split them apart using regular expressions. ...
written 5 months ago by
rmf • 690
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... I have a few bacterial whole genomes. I would like to alignment them to each other (multiple sequence alignment) and interactively explore the alignment/bases along with annotations. I have fasta genomes along with respective gff annotations. I am interested in knowing what are currently the best to ...
written 5 months ago by
rmf • 690
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... It keeps the fasta headers but seems to do some cleaning. In my case, commas (,) were converted to underscores (_). Turns out this can be turned off using ` -sformat pearson` (https://www.biostars.org/p/111857/). ...
written 5 months ago by
rmf • 690
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Answer:
A: PacBio merge runs
... I managed to get it to work. Not sure if this is the best way.
I converted `*.bax.h5` to BAM separately for each run.
bax2bam -o "sample1_run1" $(find . -name "*.bax.h5")
bax2bam -o "sample1_run2" $(find . -name "*.bax.h5")
This creates scraps and subreads BAM files. I merged the subread ...
written 7 months ago by
rmf • 690
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