User: theodore.georgomanolis

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Posts by theodore.georgomanolis

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Comment: C: in diffbind dba.peakset what is the meaning of minOverlap?
... And another question will be: if I would like to include to the resistant/ responsive only the ones that are foe example above fold change of 2 ( the Fold in your case is log2?) how could I accomplish that? Over all this is something that is been done in the Volcano plots. ...
written 9 weeks ago by theodore.georgomanolis0
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Comment: C: in diffbind dba.peakset what is the meaning of minOverlap?
... Hi Rory, thank you getting back at me. this dataset has already been under count/contrast/analyze, so your assumption is correct. the scripts you provided worked. this work perfectly. I am probably confused or did not comprehend the following part from the tutorial > 6.3 A complete occupancy a ...
written 9 weeks ago by theodore.georgomanolis0
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Comment: C: diffbind plotVenn by Factor
... Hi Rory, I did try that and I get the following: > dba.plotVenn(CHIP_seq_Goett_peaks_ALL, consensus=DBA_FACTOR) Error in dba.plotVenn(CHIP_seq_Goett_peaks_ALL, consensus = DBA_FACTOR) : unused argument (consensus = DBA_FACTOR) > dba.plotVenn(ATAC_seq_Goett_peaks, cons ...
written 9 weeks ago by theodore.georgomanolis0
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in diffbind dba.peakset what is the meaning of minOverlap?
... What will be the best use of the dba.peakset and minOverlap to extract 3 datasets that have the common peaks, the peaks enriched in c-Jun ChIP and the ones enriched in JunB ChIP. my dataset looks like: CHIP_seq_Goett_peaks_ALL 4 Samples, 33031 sites in matrix: ID Tissue ...
diffbind chip-seq dba.peakset written 9 weeks ago by theodore.georgomanolis0 • updated 7 weeks ago by Rory Stark3.0k
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Comment: C: DeSeq2 Design (A-B)-(C-D)
... by writing (A-B)-(C-D) are you looking to test the differences between the commonly expressed genes of A/B Vs the ones from C/D? ...
written 9 weeks ago by theodore.georgomanolis0
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Comment: C: DeSeq2 Design (A-B)-(C-D)
... is it possible to provide an example? thank you ...
written 9 weeks ago by theodore.georgomanolis0
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diffbind plotVenn by Factor
... Hi all, so I got the following from ATAC-seq samples > ATAC_seq_Goett_peaks 11 Samples, 47306 sites in matrix: ID Tissue Factor Replicate Caller Intervals FRiP 1 Cell1px8old epithelial Cell1 1 counts 47306 0.19 2 Cell1_3rd epitheli ...
diffbind plotvenn written 9 weeks ago by theodore.georgomanolis0 • updated 9 weeks ago by Rory Stark3.0k
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Comment: C: diffbind dba.plotvolcano bLabels option use genames instead of numbers
... this is true, although the dogma since the GREAT/bedtools days is the closest gene is the relevant one. Although all the looping data do or do not confirm it. ...
written 3 months ago by theodore.georgomanolis0
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Comment: C: diffbind dba.plotvolcano bLabels option use genames instead of numbers
... Thank you Roy for the answer, do you plan to implement an option as such? ...
written 3 months ago by theodore.georgomanolis0
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Answer: A: Normalized count in edger
... I recently found those explanatory videos that are quite helpful. in the same series there is a DeSeq2 tutorial [StatQuest: edgeR, part 1, Library Normalization][1] [1]: https://www.youtube.com/watch?v=Wdt6jdi-NQo edit: fixed wrong links and description ...
written 5 months ago by theodore.georgomanolis0

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Popular Question 2.9 years ago, created a question with more than 1,000 views. For FourCseq - error countFragmentOverlaps()

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