User: juls

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juls0
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Posts by juls

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Comment: C: Create count matrix with featureCounts for stranded as well as reversely strande
... Thank you! this would be great. ...
written 5 months ago by juls0
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Comment: C: Create count matrix with featureCounts for stranded as well as reversely strande
... Thank you for this! If I have two different protocols (RF and FR), I would need to create two separate count matrices though? It would be nice if featureCount accepts a vector for strandSpecific so one could specify the protocol for each bam file.    ...
written 5 months ago by juls0
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Create count matrix with featureCounts for stranded as well as reversely stranded, singles as well as paired-end libraries
... Hi all, I am analysing some public stranded RNA-seq data. Most are paired-end. Some libraries are  fr-secondstrand (FR / F) and most are fr-firststrand (RF / R). I have now mapped all libraries with HISAT2 using the correct --rna-strandness parameter (RF, R, F, FR). Now I would like to use featureC ...
rsubread written 5 months ago by juls0 • updated 5 months ago by Gordon Smyth35k
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ReactomePA enrichMap function - a question regarding the connections between nodes
... Dear all, Using the ReactomePA package I have visualised the enrichment results by means of the enrichMap function (for an example see the original publication, Figure 1 http://pubs.rsc.org/en/content/articlepdf/2016/mb/c5mb00663e). I am wondering though what the connections between the nodes mean ...
reactomepa written 14 months ago by juls0 • updated 14 months ago by Lluís R370
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Comment: C: ReactomePA gsePathway - a couple of questions regarding the input and output
... Thank you for your answer! ...
written 17 months ago by juls0
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Comment: C: ReactomePA gsePathway - a couple of questions regarding the input and output
... I am sorry - I am not sure I understand correctly. So you are saying I can use both - fold changes as well as log2 fold changes in the gsePathway function - and the results are different due to the way they are used in the calculations?      ...
written 17 months ago by juls0
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Comment: C: ReactomePA gsePathway - a couple of questions regarding the input and output
... Thank you for your quick reply. Just one more follow-up question - why are the results different? ...
written 17 months ago by juls0
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Comment: C: ReactomePA gsePathway - a couple of questions regarding the input and output
... Thanks for the link. I briefly read the paper related Bioconductor package (http://pubs.rsc.org/en/content/articlepdf/2016/mb/c5mb00663e) and couldn't find it.  Relating to the second question: do you mean I can use both? Either FC or log2FC? The results are different.      ...
written 18 months ago by juls0
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ReactomePA gsePathway - a couple of questions regarding the input and output
... Dear all, I have a couple of questions regarding the input and output of the gsePathway function:  1) In the resulting data frame - what is NES, core enrichment and what is the rank? 2) Should I use the fold changes or the log2FC in the gsePathway function? Thank you very much for your help! Bes ...
reactomepa written 18 months ago by juls0
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Comment: C: Adjust for multiple batches using combat
... Thanks again! It was suggested previously as a solution to Combat not being able to handle multiple batches, but I did not feel very confident about it.    ...
written 18 months ago by juls0

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