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gseabase msigdb genesetcollection Tutorial

2.9 years ago t.kuilman 170

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clusterprofiler GSEA MSIGDB

updated 3.1 years ago by Guangchuang Yu ★ 1.2k • written 3.2 years ago by thomasjenner333 • 0

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limma romer msigdb

updated 5.7 years ago by James W. MacDonald 56k • written 5.7 years ago by Jon Manning ▴ 40

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category gostats msigdb hypergeometric test

5.8 years ago petyuk ▴ 70

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Answer: DiffBind by Rory Stark ★ 3.8k

I'll answer the second question first. You should not accessing the `$binding` matrix directly -- the chromosome names are factor numbers,…

Comment: How to download the ChAMP dependency ChAMPdata by shepherl 2.6k

You could try increasing the timeout limit for downloading files. I increased mine in a `.Rprofile` script so its persistent in all sessio…

Comment: DiffBind reporting error by Rory Stark ★ 3.8k

If you could give me access to your `dbind_de` object, I can have a look at what is going on. it would help to see the sequence of calls yo…

Comment: limma - removing samples? by RMP87 • 0

Thank you very much for the explanation. Making it more precise. Could I analyze and normalize all samples from a dataset even though I had…

Comment: DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ? by Saulius • 0

Yes - I think you are right once more. Thanks for taking so much time to look into this. Size factors come in twice in the code of `cqn`: …

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What does dba.PCA in DiffBind exactly do?

Answer: How to retrieve peak summit from DiffBind peaks

Comment: How to download the ChAMP dependency ChAMPdata

Effect of feature number on adjusted p-values

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