User: Jon

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Jon90
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Posts by Jon

<prev • 104 results • page 1 of 11 • next >
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How to make clusters in heat map using ggplot2?
... Hey there, How can I cluster the heat map using ggplot2? I know already ggplot2 doesn't contain clustering, but is there any way to do that? and which is the best and easy package to plot heatmap in R? (should have color key, clustering) ...
R rna-seq written 26 days ago by Jon90
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Comment: C: How much importance is RNAseq experimental bias?
... okay, but the amount of RNA from 5 brains will be different from 6 brains right? When I look at the read counts/TPM matrix, column sums are higher in the sample pool of brains than 5 brains. ...
written 4 weeks ago by Jon90
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Comment: C: How to find correlation between two datasets/vectors?
... 1. I'm not sure why I'm getting Heatmap like this. This code is not working, only for this data. z<- output; zz<- melt(as.matrix(z)) ggplot(data = zz, aes(x=Var2, y=Var1, fill=value)) + geom_tile() [heatmap][1] 2. And also If I plot the matrix and transpose of ma ...
written 4 weeks ago by Jon90
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Comment: C: How to find correlation between two datasets/vectors?
... That's TRUE, thanks.... ...
written 4 weeks ago by Jon90
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Comment: C: How to find correlation between two datasets/vectors?
... Thanks for the beautiful explanation, but my doubt is.. the row names(genes) of those two matrix is not in the same order. My intention is to find whether the gene expression pattern is same or not. I used this, I'm not sure it whether it will stay in same order while using cor.test() x< ...
written 4 weeks ago by Jon90
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Comment: C: How to find correlation between two datasets/vectors?
... okay, Thanks a-lot! How can I make sure whether the cor.test function exactly find correlation between two matrix with same order of genes? (as they are two different data-frames, I'm afraid if the order is wrong!) my code is below, x is one matrix, y is another. for (j in 1:length(x) ...
written 4 weeks ago by Jon90
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Comment: C: How to find correlation between two datasets/vectors?
... thanks for enlightening me! but the problem is they are from different platform, one is single cell ,another is ribotag seq. here's my explanation [enter link description here][1] [1]: https://www.biostars.org/p/373019/#374978 ...
written 4 weeks ago by Jon90
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Comment: C: Is there a way to compare single-cell RNA seq and Ribotag-seq?
... Hi Devon, I got Dynamically regulated genes across the maturation trajectory(for single cell data), around 1000 genes, with 24 pseudo-time points. I have calculated correlation (spearman's/Pearson) between each ribotag data and all the pseudotime points. (to find which pseudo time expression patte ...
written 4 weeks ago by Jon90
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Comment: C: How to find correlation between two datasets/vectors?
... thanks, how can I show whether it has "similar expression pattern" ...
written 4 weeks ago by Jon90
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How to find correlation between two datasets/vectors?
... Hi there, I have two datasets. Matrix A of six columns and 300 rows. Matrix B of 12 columns and 300 rows. I want to find correlation between (each) one column of matrix A and all the columns of Matrix B. Basically to show which column of Matrix B has similar expression pattern as Matrix A. Can a ...
rna-seq written 4 weeks ago by Jon90

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Popular Question 4 weeks ago, created a question with more than 1,000 views. For MAPQ values are 60 in bwa mem
Centurion 4 weeks ago, created 100 posts.
Popular Question 13 months ago, created a question with more than 1,000 views. For How to get --transcript-to-gene-map in RSEM?
Popular Question 13 months ago, created a question with more than 1,000 views. For bwa mem has more MAPQ values as 0 and 60
Popular Question 13 months ago, created a question with more than 1,000 views. For how to sum up the columns to remove the duplicated row names in RSEM output?
Popular Question 13 months ago, created a question with more than 1,000 views. For converting paired end reads to single end, is this a good idea?
Popular Question 13 months ago, created a question with more than 1,000 views. For BWA MEM vs BOWTIE2 , which is best?
Popular Question 13 months ago, created a question with more than 1,000 views. For ERR: Perplexity is too large in Reducedimension step in Monocle
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