Bioconductor Bedtools

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granges bedtools intersect

updated 6.5 years ago by lee.s ▴ 70 • written 6.5 years ago by Bogdan ▴ 670

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3.2k

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diffbind chipseq counts peaks bedtools

updated 3.8 years ago by Rory Stark ★ 5.2k • written 6.9 years ago by Ni-Ar ▴ 10

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1.2k

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parclip bedtools bed files gff3

7.1 years ago linuxborg2 • 0

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2.1k

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bed files bedtools filtering chipseq

updated 7.2 years ago by Aaron Lun ★ 28k • written 7.2 years ago by rbronste ▴ 60

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1.6k

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HelloRanges bedtools

7.8 years ago bioinf ▴ 10

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2.6k

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summarizeoverlaps bedtools

9.0 years ago tmartinez • 0

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Comment: DepMap data mismatch by Laurent Gatto 1.6k

It might be due to different versions. The repacked/cleaned data in the `depmap` R/Bioconductor package is old, but the latest files can al…

Comment: Conumee2 - CNV.summaryplot() by James W. MacDonald 68k

If you are using `conumee2`, then you are in the wrong place. That isn't a Bioconductor package (yet? No idea if they have/will submit it).

Answer: myvariant error by James W. MacDonald 68k

You don't show anything about the data you are annotating, so it's hard to say what the problem might be. Does the example data work for yo…

Answer: Conumee2 - CNV.summaryplot() by James W. MacDonald 68k

There doesn't appear to be a function called `CNV.summaryplot` in `conumee`. What package does that function come from?

Comment: Use of limma R package with targeted proteomics for DE analysis by svlachavas ▴ 840

Dear Gordon, thank you for returning back ! Actually the output is not "NPX"-as indeed it most frequent output for a lot of pannels-but as …

Votes

A: What is the "linear model" part used for in Limma?

Comment: Use of limma R package with targeted proteomics for DE analysis

A: Unbalanced experiment with multiple samples from each patient.

Unbalanced experiment with multiple samples from each patient.

Answer: Vertical line at A=0, nothing else, on MA plot

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