User: F

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F3.1k
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I am learning everyday

Posts by F

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Comment: C: Connecting clusters of cells in 2 adjacent time points.
... Thank you, Actually I only have name of cells in cluster, expression values of genes for each cluster and markers genes specific to each cluster. In matlab code part 5 says that > Calculate a distance matrix between every child cell and parent cell (earlier and later time points) afterwar ...
written 10 days ago by F3.1k
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Comment: C: Connecting clusters of cells in 2 adjacent time points.
... Thank you Kevin, I have to go through that thoroughly; Likely here you are connecting genes to each other but in my case I must connect cluster of cells to each other where each cluster of cells has its own expression matrix and marker genes. Based on my second heat map if HIGH is the first time p ...
written 10 days ago by F3.1k
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Connecting clusters of cells in 2 adjacent time points.
... Hi, I am doing single cell RNA-seq I have 9 time points and roughly 200 cells in each time point; There is no a control-treatment assay rather I am working with a developmental process. Cells from a growing unicellular mold (Time point 0) are being starved and single cell sequencing on cells harves ...
urd R adjacency matrix igrap seurat written 11 days ago by F3.1k
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Comment: C: How I could solve this error
... Thank you but I have already tried this > sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.6 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks ...
written 19 days ago by F3.1k
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A permanent error with densityClust package
... Hi, Whatever I am trying to work with densityClust R package, I am facing this error > irisClust <- densityClust(irisDist, gaussian=TRUE) Distance cutoff calculated to 0.2767655 Error in .Call("_densityClust_gaussianLocalDensity", PACKAGE = "densityClust", : "_densityClu ...
R densityclust written 19 days ago by F3.1k
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Comment: C: The inconsistency of bulk and single cell RNA-seq results
... Thank you for your time and kindly considerations ...
written 5 months ago by F3.1k
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Comment: C: The inconsistency of bulk and single cell RNA-seq results
... Thank you, Convincing As many genes can be incorrectly read out as a zero in single cell RNA-seq, what would be a good normalization method for distinguishing more narrowly defined cell states such as cell cycle phase or stress responses, and discriminating very similar cell subtypes that differ on ...
written 5 months ago by F3.1k
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Answer: C: Construction of the coexpression network
... Reading your normalized gene expression data in r which has been saved as .txt and genes are in rows and samples are in columns mycounts <- read.table("data.txt", header = T, sep = "\t",row.names = 1) # watching the head of uploaded file head(mycounts[,1:4]) # wat ...
written 6 months ago by F3.1k • updated 6 months ago by zx87545.4k
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Comment: C: Finding genes differently expressed in time series data
... Sorry, Finally I was able to run your tutorial on my data. I used two separate weighted adjacency matrices of control and treatment data (each 26 samples and 50 genes and I used genes as nodes). my output matrices are not identical rather I can't understand how use the output to find which parts o ...
written 6 months ago by F3.1k
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Comment: C: Making a list of adjacencies
... As @Jean-Karim Heriche suggested in his tutorial, I firstly wrote my adjacency as a file in a directory, I then ran his code so ## Get list of adjacency matrices ## Each matrix is in a csv file fileList <- dir(path=dataDir,pattern = ".csv") ## Read all adjacency matrices into an array ...
written 6 months ago by F3.1k

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