User: jivarajivaraj

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Posts by jivarajivaraj

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Comment: C: Is it possible to make a PCA plot for samples using TPM exprssion values in R?
... I think you can do so library(scater) example_sce <- SingleCellExperiment( assays = list(counts = matrix of your raw values)) cpm(example_sce) <- calculateCPM(example_sce) example_sce <- normalize(example_sce) plotPCA(example_sce) You can do many th ...
written 5 weeks ago by jivarajivaraj40
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Comment: C: Showing the expression of a set of genes as 0 , 1 binaries
... Thanks a lot, I think we are somehow close to the solution; You know, I can not put a distinct threshold for each cell in a big matrix as you defined for 3 cells. matrixStats package either by colQuantiles, colRanges or colRanks functions returns values between 0 and 1 while I need either 0 or 1. No ...
written 5 weeks ago by jivarajivaraj40
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Comment: C: Showing the expression of a set of genes as 0 , 1 binaries
... Thanks a lot, for example we have cells 1 to 3 and genes A to E CELL1 CELL2 CELL3 A 0.0 1.0 1.0 B 0.0 1.0 0.0 C 0.0 1.0 0.0 D 1.0 0.0 1.0 E 1.0 1.0 1.0 Ratio 0.4 0.8 0.6 > Based on a threshold the ...
written 5 weeks ago by jivarajivaraj40
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Showing the expression of a set of genes as 0 , 1 binaries
... Hi, Usually, when we are trying to plot the marker intensities in a heat map or feature plot, they have strongly skewed distributions with varying ranges of expression, thus making it difficult to distinguish between the negative and positive cell populations. It is common practice to transform mar ...
R featureplot seurat heatmap written 5 weeks ago by jivarajivaraj40 • updated 5 weeks ago by RamRS18k
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Comment: C: Adding column annotation to heatmap using Complexheatmap
... Sorry Kevin, if I have two time points of single cell RNA-seq data, in time point 1 cells can be clustered to 2 clusters, Lets say for example in time point 1, cell1, cell9, .. (99 cells) placed in sub cluster 1, cell4, cell12,,, (34 cells) in sub cluster 2. I have also 2 sub-clusters for time poin ...
written 10 weeks ago by jivarajivaraj40
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Selecting the highest Pearson correlation coefficient of two matrices
... Hi, I have two matrices of normalised gene expression values from single cell data from two time points. In rows I have the same genes but cells in each matrix is not same(different time point). In figure 2 C of this paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5668937/ authors say they have ...
R single cell rna-seq correlation written 10 weeks ago by jivarajivaraj40 • updated 5 weeks ago by Kevin Blighe30k
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Comment: C: Extracting rows based on specific string in a column
... But all comes from heart, for example genomax I never seen to close abruptly he tries to help if not leave me with another members does not matter the country I am but I believe for hours I am searching in google GENE ID Gene Name Synonyms Gene products DDB_G0267364 DDB_G0267364_RTE ...
written 10 weeks ago by jivarajivaraj40
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Comment: C: Extracting rows based on specific string in a column
... I also wonder why you are always rushing to close the posts more than another moderators? May be sometimes later somebody wants to help, I have already searched StackOverflow and Google and for sure if my answer was there I did not create a question here ...
written 10 weeks ago by jivarajivaraj40
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Comment: C: Extracting rows based on specific string in a column
... Sorry but I have already tried some links > dat[dat$products %like% "transcription factor",] [1] GENE ID Gene products <0 rows> (or 0-length row.names) while I know there are 170 transcription factor string in products column Sorry whatever I am trying to re ...
written 10 weeks ago by jivarajivaraj40
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Comment: C: Extracting rows based on specific string in a column
... In products column for some gene there is transcription factor phrase/string ...
written 10 weeks ago by jivarajivaraj40

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