User: Hesh

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Hesh0
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Location:
University of Washington
Last seen:
4 months, 1 week ago
Joined:
10 months ago
Email:
h*******@uw.edu

Posts by Hesh

<prev • 9 results • page 1 of 1 • next >
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Comment: C: How to extract overlapping and unique peaks from the Venn Diagram to a csv forma
... I'm having trouble converting the output GRanges file to a CSV file. I did try a couple different methods to convert the GRanges to a CSV or BED file but I keep getting errors. Highly appreciate if you can let me know how to get the output in CSV format.  Thank you!   This is what I tried:  gr & ...
written 5 months ago by Hesh0
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Comment: C: How to extract overlapping and unique peaks from the Venn Diagram to a csv forma
... Thank you!  ...
written 5 months ago by Hesh0
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How to extract overlapping and unique peaks from the Venn Diagram to a csv format in DiffBind?
... Hi,  I have differential binding analysis performed on a set of samples and plotted a Venn diagram (using DiffBind) to look at overlapping and unique diff. bound sites. Now I want to get those peaks in the Venn Diagram as a list for further analysis and to look on IGV. How can I convert these data ...
diffbind plotvenn written 5 months ago by Hesh0 • updated 5 months ago by Rory Stark2.5k
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Answer: A: Using HOMER called peaks in DiffBind
... Thanks a lot! ...
written 9 months ago by Hesh0
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Using HOMER called peaks in DiffBind
... Hi,  Can I use HOMER called peaks in DiffBind without making any changes to the peaks file (HOMER output file)?   Thank you   ...
diffbind homer written 9 months ago by Hesh0
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Answer: A: Analyzing data without replicates using DiffBind
... Thank you for the explanation! Appreciate a lot!  ...
written 10 months ago by Hesh0
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Answer: A: Analyzing data without replicates using DiffBind
... Thank  you for the explanation!  Ideally for a good analysis to get statistically significant output, would you use 3 replicates per sample or 2 would be sufficient?  ...
written 10 months ago by Hesh0
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Answer: A: Analyzing data without replicates using DiffBind
... Hi Gord,  Yeah, I get it. Thank you for the quick response.  One more question: I fed the sample sheet with the four peaksets (two histone modifications in WT and NL cells). Then did: me1and2_WTvsNL <- dba.contrast(me1and2_WTvsNL, categories=DBA_CONDITION, minMembers =2) This gave a list of p ...
written 10 months ago by Hesh0
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Analyzing data without replicates using DiffBind
... Hi,  I have a ChIP-seq dataset which contains two histone modifications (me1 and me2), both mapped in WT and mutant cells. I don't have replicates for any of those. Before I do more replicates, I want to test if there are any significant differential binding events between WT and mutant cells for b ...

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