User: liruiradiant

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Posts by liruiradiant

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Comment: C: Diffbind GLM Design
... I think when Input was not specified in the meta data, then '1' is used. When Input is provided, '2' is used? ...
written 24 days ago by liruiradiant0
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Comment: C: DiffBind block not working for me
... Thanks Rory! I replaced method=db.counts$config$AnalysisMethod, to DBA_DESEQ2_BLOCK and everything works well now! ...
written 5 weeks ago by liruiradiant0
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Comment: C: DiffBind block not working for me
... Thanks Rory! I replaced method=db.counts$config$AnalysisMethod, to DBA_DESEQ2_BLOCK and everything works well now! ...
written 5 weeks ago by liruiradiant0
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DiffBind block not working for me
... Hello Rory, I have the following experimental design, Rep1 and Rep2 are collected in different batches, with batch effect obvious from PCA plots: Sample Condition Replicate 1 A 1 2 A 2 3 B 1 4 ...
diffbind written 5 weeks ago by liruiradiant0 • updated 5 weeks ago by Rory Stark3.0k
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Diffbind GLM Design
... Hello Rory, Thanks for the Diffbind package, it makes DB analysis very easy. However, I have the following question: How does DiffBind handle Input samples and how does it compare condition B with condition A? For example, I have a experiment design like this: Condition A B IP ...
diffbind written 5 weeks ago by liruiradiant0 • updated 24 days ago by Rory Stark3.0k
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Comment: C: trackViewer, the interactive version, can't view negative values in bigWig
... Thanks a lot! I can visualize negative values now. ...
written 4 months ago by liruiradiant0
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Comment: C: trackViewer, the interactive version, can't view negative values in bigWig
... Thanks a lot! I can visualize negative values now. ...
written 4 months ago by liruiradiant0
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How to get 'shortest' distance with ChIPpeakAnno::binOverFeature
... Dear Jianhong, I'm working on a project to plot the distance between Differentially Methylated Cytosine (DMC) to CpG islands. The DMC are just 1bp wide, and the CpG islands has width. I want to get the shortest distance between DMC and CpG. That is, if the relative location is `DMC------distance ...
chippeakanno written 4 months ago by liruiradiant0
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Comment: C: trackViewer, the interactive version, can't view negative values in bigWig
... That is great. Thank you so much!!! Ray ...
written 4 months ago by liruiradiant0
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Comment: C: trackViewer, the interactive version, can't view negative values in bigWig
... Hello Jianhong, I'm helping biologists to use the web application of trackViewer, where we downloaded the docker image and started the GUI. I think we don't have the access to under-the-hood R objects from there. Also, we had both positive and negative values in our bigWig files, and that repres ...
written 4 months ago by liruiradiant0

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