User: mk

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mk50
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Posts by mk

<prev • 17 results • page 1 of 2 • next >
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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 9 weeks ago by mk50
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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 3 months ago by mk50
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specify a root in igraph minimum-spanning-tree
... I have a weighted adjacency matrix and I need to create a directed MST. The problem is that I know the edge weights and the root, so I can generate an MST on an undirected graph, but I cant find a way to then specify a root. If I could specify a root, this would automatically induce directions on ...
R minimum-spanning-tree directed-graph igraph written 4 months ago by mk50 • updated 3 months ago by Biostar ♦♦ 20
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How to reproduce MATLAB tsne('algorithm', 'exact') result in R?
... Given: 1. a 25x25 matrix of integers 2. an initial 25x3 embedding, generated by PCA 3. perplexity 2 4. random seed set to 1 5. target embedding dimension 3 Run exact t-SNE using MATLAB tsne('algorithm', 'exact') and R Rtsne(theta = 0) Here is the data "A": 0 0 0 0 0 97 0 0 0 0 0 0 0 93 ...
tsne pca matlab R rtsne written 4 months ago by mk50
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Mapping Ensembl Gene IDs with dot suffix
... I have a bunch of bulk mRNA sequencing pulled off of the TCGA. Feature names appear to be Ensembl gene IDs with a suffix. Here is an example: > [995] "ENSG00000236246.1" "ENSG00000281088.1" [997] "ENSG00000254526.1" "ENSG00000223575.2" [999] "ENSG00000201444.1" "ENSG00000232573.1" I ...
gene ensembl biomart bioconductor written 10 months ago by mk50 • updated 8 months ago by PavolG0
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kmeans error when running reduceDimension(reduction_method = 'DDRTree')
... After setting my ordering filter, I run: > colonTumor <- reduceDimension(colonTumor, max_components = 3, > norm_method = c("none"), reduction_method = 'DDRTree', verbose=TRUE) Then I get the following error: > Error in kmeans(t(Z), K, centers = centers) : initial centers are not > ...
irlba monocle kmeans ddrtree written 11 months ago by mk50 • updated 11 months ago by Kevin Blighe35k
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Answer: A: Creation of cellDataSet in Monocle 2 wants undocumented AnnotatedDataFrame: assa
... turned out that fd was prepared based on a bad matrix. Issue resolved! ...
written 12 months ago by mk50
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Creation of cellDataSet in Monocle 2 wants undocumented AnnotatedDataFrame: assayData
... As directed in the [Monocle 2 Documentation][1], the cellDataSet constructor is called on a sparse matrix and two AnnotatedDataFrames. Here is the suggested usage: pd <- new("AnnotatedDataFrame", data = sample_sheet) fd <- new("AnnotatedDataFrame", data = gene_annotation) cds < ...
celldataset monocle expressionset written 12 months ago by mk50
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Processor count for cores with Intel hyper-threading in differentialGeneTest()
... The documentation for Monocle 2 discusses the use of multiple cores for differential gene expression. Will I be able to use each virtual core on a hyper-threaded processor? For instance, if I had an 8-core Xeon W, would I be able to make the following call: differentialGeneTest(, cores=14) D ...
hpc monocle hyperthreading rna-seq written 12 months ago by mk50 • updated 12 months ago by himanshuarya91620
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Given two sets of nucleotide n-mers, how can I learn sets of 'motifs' which are present in one and not the other?
... I have some unpublished data on DNA methylation, suggesting that there are differences in maintenance methylation efficiency at different sites from one cell cycle to another. I have a very coarse-grained approach for dividing the methylated sites into "likes to be methylated" and "really likes to ...
sequencing tf dna-methylation written 13 months ago by mk50

Latest awards to mk

Popular Question 4 weeks 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 7 weeks 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 7 weeks ago, asked a question with at least 3 up-votes. For Mapping Ensembl Gene IDs with dot suffix
Scholar 12 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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