User: F

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F3.0k
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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 22 days ago by F3.0k
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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 22 days ago by F3.0k
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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 weeks ago by F3.0k • updated 6 weeks ago by zx87544.3k
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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 7 weeks ago by F3.0k
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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 7 weeks ago by F3.0k
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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 7 weeks ago by F3.0k
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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 8 weeks ago by F3.0k
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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 8 weeks ago by F3.0k
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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 8 weeks ago by F3.0k
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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 8 weeks ago by F3.0k

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