User: Lucy

gravatar for Lucy
Lucy40
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40
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New User
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Last seen:
2 months, 4 weeks ago
Joined:
1 year, 7 months ago
Email:
l**********@merton.ox.ac.uk

Posts by Lucy

<prev • 49 results • page 1 of 5 • next >
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Comment: C: findGenomeMotif.pl in Homer couldn't work properly
... Hi, Did you ever solve this? I have the same problem. Many thanks, Lucy ...
written 3 months ago by Lucy40
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Comment: C: problem with HOMER findMotifsGenome.pl
... Hi, I am having the same problem. Did you ever work out what the problem was? Many thanks, Lucy ...
written 3 months ago by Lucy40
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Comment: C: Which counts to use for RNA-seq heatmap and PCA?
... `heatmap.2(tmm_log, trace = "none", col = bluered(20), scale = "row")` ...
written 3 months ago by Lucy40
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Comment: A: Which counts to use for RNA-seq heatmap and PCA?
... Thank you, I am currently scaling by row using the heatmap.2 function from the gplots package. Is this an acceptable way to do the scaling? ...
written 3 months ago by Lucy40
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Which counts to use for RNA-seq heatmap and PCA?
... Hi, I have RNA-seq data that I would like to visualise with a PCA plot and a heatmap. I am wondering whether I should use normalised or log transformed normalised counts for this. I have generated TMM-normalised counts per million in EdgeR as follows: y <- calcNormFactors(y) tmm <- ...
pca rna-seq edger heatmap written 3 months ago by Lucy40
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Comment: C: biplot scaling options (ggbiplot)
... Ok thank you for the advice. ...
written 4 months ago by Lucy40
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Comment: A: biplot scaling options (ggbiplot)
... Thank you for suggesting PCAtools - I will try this out. Why do you set obs.scale and var.scale to 1 in the command above? If you change obs.scale, it seems to modify the PC1 axis, while changing var.scale modifies the loading arrows. ...
written 4 months ago by Lucy40
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biplot scaling options (ggbiplot)
... Hi, I have a prcomp object (generated using the prcomp function) and I am trying to generate a biplot using ggbiplot, however I am confused about the different scaling options and their impact on the meaning of the plot. ggbiplot(pcobj, choices = 1:2, scale = 1, pc.biplot = TRUE, obs.scale = ...
biplot pca ggbiplot written 4 months ago by Lucy40
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Comment: C: DEsingle differential-expression analysis
... Ok thank you. I did try asking on their GitHub but I haven't had a response. ...
written 4 months ago by Lucy40
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DEsingle differential-expression analysis
... Hi, I am running DEsingle (https://pubmed.ncbi.nlm.nih.gov/29688277-desingle-for-detecting-three-types-of-differential-expression-in-single-cell-rna-seq-data/) to compare two clusters of cells identified by Smart-seq2 scRNA-sequencing. I have filtered the genes before running DEsingle to retain on ...
scrna-seq differential-expression analysis written 4 months ago by Lucy40

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Popular Question 12 months ago, created a question with more than 1,000 views. For FRIP score ATAC-seq

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