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Question: R package for Meta-Analysis of CHIP-Seq data
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gravatar for rezapanahi222
5 months ago by
rezapanahi2220 wrote:

hi  everyone

i am new in chip-seq analysis

i did a chip-seq analysis by command line(UBUNTU)

and i want to do a Meta -analysis to integrative all study that dirived from my analysis

but i do not know which package do it ????

please help me

thanks

 

ADD COMMENTlink modified 5 months ago • written 5 months ago by rezapanahi2220
1
gravatar for Aaron Lun
5 months ago by
Aaron Lun17k
Cambridge, United Kingdom
Aaron Lun17k wrote:

Your question is too vague. How did you do the "analysis"? Peak-calling? What kind of "meta-analysis" do you want to do? If you're trying to look for differences between samples, googling "differences chip-seq bioconductor" will already give a number of relevant hits.

ADD COMMENTlink written 5 months ago by Aaron Lun17k

i did a peak-calling analysis  by macs2.

i want to (meta-analysis) look for differences between samples.

What software or methods can I use?

ADD REPLYlink modified 5 months ago • written 5 months ago by rezapanahi2220
1
gravatar for Rory Stark
5 months ago by
Rory Stark2.1k
CRUK, Cambridge, UK
Rory Stark2.1k wrote:

If you want to use your MACS2 peaks, the DiffBind package offers a straightforward path to identifying differentially bound peaks. The csaw package is another alternative, particularly if your dataset requires more sophisticated normalization.  In either case the original BAM files are required. 

Cheers-

Rory

ADD COMMENTlink written 5 months ago by Rory Stark2.1k
0
gravatar for rezapanahi222
5 months ago by
rezapanahi2220 wrote:

i mean that i did chip-seq analysis data with command line on ubuntu

i used the MACS2 peak caller for obtain the peakset files .

now i want to finde a package that integrate my peakset data (obtained from macs2 ) in multiple study .

which tools or package that i used is good ???

i hope that it is simly

cheers

 

ADD COMMENTlink written 5 months ago by rezapanahi2220
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