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: The inconsistency of bulk and single cell RNA-seq results
... Thank you for your time and kindly considerations ...
written 3 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 3 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 4 months ago by F3.1k • updated 4 months ago by zx87544.8k
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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 4 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 4 months ago by F3.1k
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Making a list of adjacencies
... Hi, I have two adjacency matrices like so; > head(a[,1:4]) 0.000000000 0.001287944 0.0009840186 0.001331908 0.009028600 0.000000000 0.0454970255 0.086481054 0.009351082 0.100214642 0.0000000000 0.084016084 0.012369094 0.101991920 ...
R factorization written 4 months ago by F3.1k
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Defining conditions in EBSeq-HMM
... Excuse me, I have cell lines treated with lead (pb) from day 1 to day 26 and 26 match controls (52 samples without replicates). I was trying EBSeqHMM for my time series so; > CondVector <- rep(paste(c("C", "L"),1:52,sep=""),each=1) > View(CondVector) **Condition ...
R rna-seq ebseq-hmm written 4 months ago by F3.1k
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Comment: C: Calculating distance matrix of RNA-seq data
... Thank you, library(dtw) I want to calculate distance matrix of my time series, I can't figure out how do that > for(i in control) { + for(j in lead) { + alignment <- dtw(control[i],control[j]) + distance[i, j] <- alignment$distance + } + } Erro ...
written 4 months ago by F3.1k
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Comment: C: Finding genes differently expressed in time series data
... Thank you, since creating this post I am googling for dtw but seems to complex. I did not get error and gives me a class 'dist' atomic you mean I should put control and lead in this code? for(i in control) { for(j in lead) { alignment <- dtw(item[i],item[j]) dist ...
written 4 months ago by F3.1k
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Comment: C: WGCNA TOM calculation time
... The most number of genes I have ever used for WGCNA was about 9000 genes (as my laptop can't afford bigger matrices), that takes less than 5 min to calculate TOM. ...
written 4 months ago by F3.1k

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