User: mk

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mk90
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Posts by mk

<prev • 25 results • page 1 of 3 • next >
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scater/scran workflow for batches recompute size factors after MNN?
... This question is in reference to the excellent tutorial posted [on bioconductor site][1] on batch correction using scran. Specifically there is a comment that reads: > Technically, we should have performed variance modelling and feature selection after calling multiBatchNorm(). This ensures th ...
R bioconductor scater scran written 5 months ago by mk90
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Comment: C: How to submit a genomics package with lots of data to CRAN
... Thanks @Satosh Anand. It looks like Dave Kleinschmidt has permanently hosted the data package in that example on github, since it can't be hosted in CRAN. I've done a bit of digging and found the following [here][1]: > Packages on which a CRAN package depends should be available from a mainstr ...
written 7 months ago by mk90
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How to submit a genomics package with lots of data to CRAN
... I've got a package that I'd like to submit to CRAN, but the data is huge, about 20 MB of compressed internal (used for unit tests, not exported) and about 7 MB of compressed exported data (used in vignettes). I could maybe cut this down a bit by altering my compression but not by much. This pack ...
R cran genomics written 7 months ago by mk90
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Comment: C: GenomicDataCommons request timeouts cases() %>% ... %>% results_all()
... @Sean Davis, thanks a lot for this info. Frankly this package is a life saver for me, since it addresses the need for general purpose GDC usage. ...
written 7 months ago by mk90
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Comment: C: GenomicDataCommons request timeouts cases() %>% ... %>% results_all()
... Ok, I threw up a link on Bioconductor forum. In case the answer gets posted there I'll update this thread. ...
written 8 months ago by mk90
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Answer: A: GenomicDataCommons request timeouts cases() %>% ... %>% results_all()
... I have a fix for this but it's not very satisfactory. Based on Sean Davis' [blog post][1] I retrieved sequencing data and extracted the case id's from that, then looped over the case ids fetching diagnosis data 50 records at a time. The fact that this worked is a mystery to me, since the query aga ...
written 8 months ago by mk90
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Comment: C: GenomicDataCommons request timeouts cases() %>% ... %>% results_all()
... Thanks @Kevin Blighe, sloppy cut/paste job I forgot to add the project to the filter() method. Edited above. ...
written 8 months ago by mk90
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GenomicDataCommons request timeouts cases() %>% ... %>% results_all()
... I've been experimenting with the [GenomicDataCommons][1] package to handle query work against the GDC API. For some reason there is an issue with timeouts for requests of a certain length. There doesn't seem to be a direct way around this using the piped syntax. Anyone else have luck with this? ...
genomicdatacommons bioconductor R http written 8 months ago by mk90 • updated 8 months ago by Sean Davis25k
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CLRS-type algorithms on sna/network
... I began using R iGraph to compute things like minimum-spanning-trees, but iGraph plotting was unsatisfactory. My search for a ggplot2-based network visualization library led me to sna/network via ggnetwork, which can utilize iGraph objects only through implicit (buggy) conversion to sna/network obj ...
graph network ggnetwork sna R written 10 months ago by mk90
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(Closed) typeset roxygen math (\eqn and \deqn content) in html output
... I use \deqn and \eqn to typeset math in roxygen function documentation. Compiling the pdf manual produces the typesetting that I want, however, I cant find a way to compile the math and embed graphics in the html pages when I run devtools::document(). Is there any known way of doing this? ...
R roxygen latex written 11 months ago by mk90

Latest awards to mk

Popular Question 7 months ago, created a question with more than 1,000 views. For GDC API query to map HT-seq FPKM UUID to a Case UUID
Popular Question 9 months ago, created a question with more than 1,000 views. For GDC API query to map HT-seq FPKM UUID to a Case UUID
Popular Question 9 months ago, created a question with more than 1,000 views. For GDC API query to map HT-seq FPKM UUID to a Case UUID
Student 9 months ago, asked a question with at least 3 up-votes. For Mapping Ensembl Gene IDs with dot suffix
Scholar 20 months ago, created an answer that has been accepted. For A: Creation of cellDataSet in Monocle 2 wants undocumented AnnotatedDataFrame: assa

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