User: Lila M

gravatar for Lila M
Lila M 240
Reputation:
240
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Trusted
Location:
UK
Last seen:
2 days, 17 hours ago
Joined:
1 year, 7 months ago
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Posts by Lila M

<prev • 138 results • page 1 of 14 • next >
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Comment: C: phylonet input tree with bootstrap
... I am afraid but I've never used phylonet. I don't know if you have to use it or you can choose another software. I recommend you to use [Figtree][1], [trex][2] .. but in this [web site][3] you can find your solution. I hope these resources could help you. ;) [1]: http://beast.bio.ed.ac.uk/figtr ...
written 5 days ago by Lila M 240
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Answer: A: Software for Tree Visualization
... As previously mentioned, there are lot of good programs. FigTree is also my favorite (http://beast.bio.ed.ac.uk/figtree). I recommended you to have a look in this web site, you will find something that will cover your needs! http://evolution.genetics.washington.edu/phylip/software.html ...
written 5 days ago by Lila M 240
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Comment: C: coverage for unique transcript and df process
... Oook, and also the function sort the df alphabetically according with trasncript (I thought that I lost some date but is the way in which is sorted). Do you know any options to respect the initial order? Thanks! ...
written 9 days ago by Lila M 240
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Comment: C: coverage for unique transcript and df process
... Yes, I've just edit my question, but the code is not working at all because it remove the duplicated. ...
written 9 days ago by Lila M 240
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coverage for unique transcript and df process
... Hi guys, I would like to process a data frame in R Chr start end strand transcript Length number_bp_overlap chr1 879583 882140 - uc031pkq 2858 297 chr1 1571100 1647617 - uc001ags 76818 270 chr1 33117259 33151812 + uc010ohk 34854 200 chr1 33117259 33151812 + uc010ohk 34854 2 ...
R coverage data frame written 9 days ago by Lila M 240 • updated 9 days ago by Rashedul Islam140
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Comment: C: DESeq2: Find differentially expressed genes specific to one condition
... you can try this: #dd is your DESeq matrix vsd <- varianceStabilizingTransformation(dd, blind=TRUE) vst <- assay(vsd) colnames(vst) <- colnames(count.table) vst <- vst - min(vst) dds <- DESeq(dd) res.AvsB <- results(dds, contrast=c("treatment","A" ...
written 10 days ago by Lila M 240
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Correct pipeline for DESeq analysis
... Hi everybody. I'm working with RNASeq data and I am relatively new in that field. I would like to know if my approach is correct or not (or how I can improve it). Assuming that I have 3 different condition or treatment (high, low and mut) what I did is: dds <- DESeqDataSetFromMatrix( ...
deseq2 rna-seq written 16 days ago by Lila M 240
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Answer: A: How to plot a heat map for the top 30 differentially expressed genes.
... What I did is: library(pheatmap) mat <- assay(vsd)[head(order(res2$padj), 50), ] class(vsd) mat <- mat - rowMeans(mat) pheatmap(mat) And, apparently, it works for me! ...
written 17 days ago by Lila M 240
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Comment: C: problems with mclapply function
... not, of course.... Thank you and sorry for this stupid question! ...
written 19 days ago by Lila M 240
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Comment: C: problems installing HTSeq
... As always Davon, problem solved :) Thank you so much! ...
written 22 days ago by Lila M 240

Latest awards to Lila M

Scholar 17 days ago, created an answer that has been accepted. For A: How to plot a heat map for the top 30 differentially expressed genes.
Centurion 9 weeks ago, created 100 posts.
Supporter 11 weeks ago, voted at least 25 times.

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