User: Gary

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Gary0
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Posts by Gary

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Principal component analysis produced by DiffBind, but PC1 with smaller variation than PC2
... Hi, I am not sure whether this question here is proper or not. If it is not, I will remove this post. I have a principal component analysis (PCA) figure below produced by DiffBind. After discussing with my colleagues, we wonder why the variation of Principal Component #1 is smaller than Principal ...
diffbind pca written 5 days ago by Gary0 • updated 2 days ago by Rory Stark2.0k
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Comment: C: How DiffBind run PCA based on peak data?
... I really appreciate your detailed and clear explanation. Gary ...
written 11 days ago by Gary0
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Comment: C: How DiffBind run PCA based on peak data?
... Thanks a lot. May I double check with you? I use macs2 to do peak calling and obtain peaks.narrowPeak (BED6+4 format) files. In this case, the peak scores DiffBind adopted is the 5th column (integer score for display), the 8th column (-log10pvalue), or the 9th column (-log10qvalue) for computing pri ...
written 11 days ago by Gary0
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How DiffBind run PCA based on peak data?
... May I know how DiffBind analyze peak present/absent data for a PCA analysis? The traditional PCA needs continuous values with the normal distribution. Does DiffBind use a non-parametric method? Or DiffBind use scores (e.g. FDR value) for each peak to perform PCA? Many thanks. ...
diffbind written 12 days ago by Gary0 • updated 11 days ago by Rory Stark2.0k
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Comment: C: There is no dba.plotVolcano function in DiffBind and how to upgrade DiffBind to
... Thanks a lot ...
written 12 days ago by Gary0
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Can ChIPQC analyze mandarin duck ChIP-Seq data?
... Hi, I am analyzing mandarin duck (Aix galericulata) ChIP-Seq data. We have a mandarin duck genome assembly .fa file and a genome annotation .gff file produced by our cooperators. May I know whether ChIPQC can analyze mandarin duck histone modification ChIP-Seq data? Could you show me how to do it, ...
chipqc written 13 days ago by Gary0
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Comment: C: There is no dba.plotVolcano function in DiffBind and how to upgrade DiffBind to
... I have installed R 3.4. However, when I run dba.report() with bDB = TRUE, and bNotDB = TRUE, I can see the corresponding values in Global Environment, but there is still no the corresponding file in my working directory (the detail below). Could you help me more? Many thanks. h3k27ac.DB <- dba.r ...
written 15 days ago by Gary0
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Comment: C: There is no dba.plotVolcano function in DiffBind and how to upgrade DiffBind to
... Many thanks ...
written 22 days ago by Gary0
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There is no dba.plotVolcano function in DiffBind and how to upgrade DiffBind to version 2.4.8
... Hi, I would like to use dba.plotVolcano function in DiffBind, but R 3.3.3 cannot find it. In addition, I found that options of bNotDb, bGain, and bLoss for dba.report don’t work in my DiffBind 2.2.12. I guess that it is because my DiffBind is not the last version, i.e. 2.4.8. However, when I instal ...
diffbind written 23 days ago by Gary0 • updated 12 days ago by Rory Stark2.0k
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Comment: C: How to set DiffBind dba.plotHeatmap colSideCols option
... Hi Rory, Thank you so much, and I am looking forward this new function. Best, Gary ...
written 23 days ago by Gary0

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