User: kushshah

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kushshah10
Reputation:
10
Status:
New User
Location:
University of North Carolina, Chapel Hill, USA
Last seen:
3 months, 2 weeks ago
Joined:
4 months, 3 weeks ago
Email:
k*******@live.unc.edu

Posts by kushshah

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Unable to change point size in plotExpression()
... Thanks Aaron. Didn't realize there were extra arguments in `scater-plot-args`. This is really helpful. In the list of extra arguments, I didn't see any way to add a chart title - is this possible for `plotExpression()`? ...
written 4 months ago by kushshah10
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Unable to change point size in plotExpression()
... Seems relatively basic, but I can't find a way to change graph dynamics using the `plotExpression()` function in `scater`. For example, I have the following gene expression plot: https://ibb.co/q9p1Zq5 I am coloring points by cell type, but there are so many points and they are too big - therefore, ...
scater singlecellexperiment plotexpression plotting written 4 months ago by kushshah10 • updated 4 months ago by Aaron Lun24k
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Comment: C: ERROR - Size factors should be positive real numbers (using normalize() function
... This is extremely helpful, thank you so much. I've also batched `isOutlier()` by individual now. Had a quick question - does "remove cells with zero spike-in size factors" mean "remove cells whose read count for every spike-in is zero"? If so, I was looking at the code you linked to. Your `for.hvg ...
written 4 months ago by kushshah10
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ERROR - Size factors should be positive real numbers (using normalize() function)
... I have a SingleCellExperiment object, and no matter what I do, when I run `normalize(filtered.sce)`, I get the error: `size factors should be positive real numbers`. It is my understanding that even though `computeSumFactors()` coerces to positive by default if necessary, it doesn't imply that `nor ...
qc scran scater singlecellexperiment normalize written 4 months ago by kushshah10
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Bioconductor with RPKM counts or Raw counts
... I am performing a scRNA-seq analysis, and will be using the SingleCellExperiment library of Bioconductor to do so. The data for the project comes in both raw and log2(RPKM) formats. Is there a preferable format to use as the input for a SingleCellExperiment object? Does this object work well with RP ...
normalization rpkm qc singlecellexperiment written 4 months ago by kushshah10 • updated 4 months ago by Aaron Lun24k
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Log2(RPKM) counts in Bioconductor
... Hi all. I have an expression matrix that consists of log2-transformed RPKM counts. When I read this matrix in to a SingleCellExperiment object, how does Bioconductor know that I am working with RPKM counts? Is there a way to specify that my counts are log2(RPKM) counts, rather than raw reads? Furth ...
R rpkm expression scater calcaverage written 4 months ago by kushshah10 • updated 4 months ago by Aaron Lun24k
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Comment: C: Getting CDSCHROM values from ENSEMBL/SYMBOL keys using mapIds from TxDb.Hsapiens
... Hi James - to answer the question you asked about how we got reads: our data is already in gene symbol format. E.g. data looks like this. We didn't have to map reads to genes because we are accessing another data source that directly provides this information: .................AZ_A1 AZ_A10 ...
written 4 months ago by kushshah10
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Comment: C: Getting CDSCHROM values from ENSEMBL/SYMBOL keys using mapIds from TxDb.Hsapiens
... Sorry - pls see comment below ...
written 4 months ago by kushshah10
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Getting CDSCHROM values from ENSEMBL/SYMBOL keys using mapIds from TxDb.Hsapiens.UCSC.hg19.knownGene
... I am new to using Bioconductor. I have a SingleCellExperiment object, sce, that contains rownames in SYMBOL format, and rowData in ENSEMBL format. Using TxDb.Hsapiens.UCSC.hg19.knownGene, I wish to find the chromosomal location for each gene (for downstream mitochondrial gene controlling) and store ...
annotationdbi ensembl org.hs.eg.db singlecellexperiment cdschrom written 4 months ago by kushshah10 • updated 4 months ago by James W. MacDonald50k

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