User: Shian Su

gravatar for Shian Su
Shian Su10
Reputation:
10
Status:
New User
Location:
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Last seen:
1 week, 2 days ago
Joined:
1 year, 10 months ago
Email:
s***@wehi.edu.au

Posts by Shian Su

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapien
... Thanks Johannes, that's very helpful. Do you know if there are any major differences between the AH##### databases and Homo.sapiens that I should be aware of? ...
written 8 weeks ago by Shian Su10
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Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapiens/Mus.musculus?
...   I'm trying to use Homo.sapiens to annotate genes from my count matrix. However I never seem to find any genes from chrM. library(Homo.sapiens) all_genes <- biomaRt::select( Homo.sapiens, key = keys(Homo.sapiens, keytype = "GENEID"), keytype = "GENEID", columns = c("CDSCHROM" ...
annotationdbi homo.sapiens written 8 weeks ago by Shian Su10 • updated 8 weeks ago by Johannes Rainer1.1k
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Comment: C: Cannot create SingleCellExperiment object
... Thanks Aaron, following that other question thread lead me to the solution. I had been drawing most of the BioC packages from a shared location I have no access to. The solution was to use biocLite("SingleCellExperiment", dependencies=TRUE, lib="~/R/library") to get a copy of all the dependencies ...
written 11 weeks ago by Shian Su10
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Cannot create SingleCellExperiment object
...   Using R 3.4.2, BioC 3.6, SingleCellExperiment_1.0.0. The following example code from ?SingleCellExperiment produces an error   library(SingleCellExperiment) ncells <- 100 u <- matrix(rpois(20000, 5), ncol=ncells) v <- log2(u + 1) pca <- matrix(runif(ncells*5), ncells) tsne <- ...
singlecellexperiment written 11 weeks ago by Shian Su10 • updated 11 weeks ago by Aaron Lun18k
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Comment: C: How do you test a contrast in MAST?
... Thanks, I guess having an intercept model is fine. Is this interface for contrasts documented anywhere? I couldn't quite work it out from the vignette and help pages. ...
written 4 months ago by Shian Su10
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How do you test a contrast in MAST?
... I am trying to analyse some single cell RNA seq data with MAST, currently I'm using an edgeR pipeline and I cannot work out how to properly test a contrast in MAST. The experimental setup is a 3x2 with 3 strains and 2 conditions, I'd like to test differential expression between the conditions withi ...
differential gene expression single-cell mast written 4 months ago by Shian Su10 • updated 4 months ago by Andrew_McDavid90
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Comment: C: Does Rhtslib currently work on Windows?
... Thanks so much Martin, the necessary code was to add `import(Rhtslib)` to the `NAMESPACE`, which I did via ROxygen's `@import` for consistency.  I still needed the `zlibbioc::pkgconfig()` code because I actually reference `zlib` directly in some of my c++. I'll post these to the dev mailing list in ...
written 5 months ago by Shian Su10
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Comment: C: Does Rhtslib currently work on Windows?
... Yes that `zlibVersion` was a typo, wasn't logged into bioconductor on my Windows testing laptop so I typed out the error message. Thanks for the help, I'll try it out once I'm infant of a Windows laptop again. ...
written 5 months ago by Shian Su10
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Does Rhtslib currently work on Windows?
... I'm helping develop scPipe which we're currently trying to contribute to Bioconductor. Unfortunately the are build issues on Windows that I am unable to resolve. Namely the package is unable to load its own DLL. I noticed that link2Rhtslib does not build on Windows with the error localfunc.o:localfu ...
package rhtslib htslib written 5 months ago by Shian Su10 • updated 5 months ago by Martin Morgan ♦♦ 21k
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Answer: C: bug in Glimma - anno can't have T/F
... Thanks for bringing this to my attention, it's definitely an unintended bug, it will be fixed in the next patch which I hope to push out by the end of the week. ...
written 19 months ago by Shian Su10

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