User: MarjoryMollusc

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New User
Location:
Australia
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1 week, 4 days ago
Joined:
3 months, 3 weeks ago
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a**********@hotmail.com

Posts by MarjoryMollusc

<prev • 19 results • page 1 of 2 • next >
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Comment: C: Can I determine the machine used for RNA-seq from the .count file extension?
... Awesome, thanks for that. I had a suspicion that would be the case! ...
written 11 days ago by MarjoryMollusc30
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Can I determine the machine used for RNA-seq from the .count file extension?
... Hi guys, I feel like this should be super obvious, but I am struggling to find anywhere online the steps to figure out what machine a data set came from. The files have a `.count` file extension on them, and are filled with ENSEMBL IDs followed by the count. an example: ENSMUSG00000000001.4 39 ...
count rna-seq written 11 days ago by MarjoryMollusc30 • updated 11 days ago by mkulecka300
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RNA-seq cluster analysis in R
... So I have my time series RNA-seq data, which I conducted some k-means clustering on in R to have a look at how it clusters. I am wondering if there are any good tools in R to then analyse the genes within each cluster, or the next step from the k-means clustering? Each cluster has around 50 genes in ...
R k-means rna-seq clustering written 26 days ago by MarjoryMollusc30 • updated 9 days ago by Zhilong Jia1.3k
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Comment: C: The RNA-Seq data input for WGCNA in terms of gene co-expression network construc
... Those are such useful links! Thanks so much for that. Just another quick (and probably stupid/obvious question), how do you deal with duplicate genes in the count matrices? Do you just collapse the counts? Or something else? If so, how would you advise collapsing them? The Ensembl symbols for the g ...
written 5 weeks ago by MarjoryMollusc30
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Comment: C: The RNA-Seq data input for WGCNA in terms of gene co-expression network construc
... Hi Kevin, Very useful answer thanks! Just a question about using this on a set of data, If I have a series of 44 samples with two levels within those 44 samples and the aim is to compare the two levels, would it be advisable to use all 44 samples in the one analysis or to separate the two and run ...
written 5 weeks ago by MarjoryMollusc30
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Comment: C: Graphing specific gene expression data from DGEList
... @Ram, thanks! With both contributions I have managed to figure out the aggregation of the data ...
written 9 weeks ago by MarjoryMollusc30
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Comment: C: Graphing specific gene expression data from DGEList
... I managed to figure that out. Thanks again! Any chance you could explain how ggplot2 could be used using the strings D0, D2, D4, D6 in column one from two dataframes to plot a similar plot as above, but with the discrete variables? I managed to figure out how to get one line in, but it is also put ...
written 9 weeks ago by MarjoryMollusc30
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Comment: C: Graphing specific gene expression data from DGEList
... Ah awesome! That's exactly what I have been trying to get. Did not know about the aggregate function. Thanks so much! The idea is to get a simple plot of expression with nothing too complicated. ...
written 9 weeks ago by MarjoryMollusc30
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Comment: C: Graphing specific gene expression data from DGEList
... Thanks for the answer, but not quite what I'm after. I'll update the question above with example data ...
written 9 weeks ago by MarjoryMollusc30
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Graphing specific gene expression data from DGEList
... I have a large set of RNA-seq expression data in a DGEList object, and I want to plot the epxression data between two factors for specific genes temporally. I started out by subsetting the data into a smaller matrix and then realised that was silly, and I should be able to plot it from the DGEList ...
ggplot2 edger rna-seq dgelist written 9 weeks ago by MarjoryMollusc30

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