Bioconductor Bedtools

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13k

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granges bedtools intersect

updated 7.4 years ago by lee.s ▴ 70 • written 7.4 years ago by Bogdan ▴ 670

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3.7k

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diffbind chipseq counts peaks bedtools

updated 4.7 years ago by Rory Stark ★ 5.2k • written 7.7 years ago by Ni-Ar ▴ 10

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1.4k

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parclip bedtools bed files gff3

8.0 years ago linuxborg2 • 0

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bed files bedtools filtering chipseq

updated 8.0 years ago by Aaron Lun ★ 29k • written 8.0 years ago by rbronste ▴ 60

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1.9k

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HelloRanges bedtools

8.6 years ago bioinf ▴ 10

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3.2k

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summarizeoverlaps bedtools

9.9 years ago tmartinez • 0

6 results • Page 1 of 1

Recent ...

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Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k

Your follow-up question is very much wider than the first, and is essentially a research question rather a software question. As one of the…

Comment: Error in creating BSGenome package by Nguyen • 0

I keep running into this error, please help: ``` Writing all sequences to './BSgenome.Panubis.NCBI.Panubis1.0/inst/extdata/single_sequenc…

Comment: Joining different datasets and analyzing using the group-specific condition effe by James W. MacDonald 68k

There is an example of how you can do this in the [DESeq vignette][1]. An alternative would be to fit a linear mixed model using the `vari…

Comment: Joining different datasets and analyzing using the group-specific condition effe by jason.chai • 0

@mikelove Could I please ask if a similar method would work my set of samples? I have 255 samples which have been generated from 76 subject…

Comment: Clarification on counting in Rsubread (featureCounts) by Luca • 0

Thanks to both of you for your helpful suggestions. The counting was already strand-specific at both the exon and gene levels. I resolved …

Votes

A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi

Answer: Clarification on counting in Rsubread (featureCounts)

Comment: Clarification on counting in Rsubread (featureCounts)

C: ControlGenes/ housekeeping genes Deseq2

Answer: Clarification on counting in Rsubread (featureCounts)

Awards • All

Commentator to James W. MacDonald 68k

Great Question to fl ▴ 20

Popular Question to Lluís Revilla Sancho ▴ 760