Question: R package for Meta-Analysis of CHIP-Seq data
0
2.1 years 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 ????

thanks

chipseq ubuntu meta-analysis • 556 views
modified 2.1 years ago • written 2.1 years ago by rezapanahi2220
Answer: R package for Meta-Analysis of CHIP-Seq data
1
2.1 years ago by
Aaron Lun24k
Cambridge, United Kingdom
Aaron Lun24k 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.

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?

Answer: R package for Meta-Analysis of CHIP-Seq data
1
2.1 years ago by
Rory Stark2.8k
CRUK, Cambridge, UK
Rory Stark2.8k 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

Answer: R package for Meta-Analysis of CHIP-Seq data
0
2.1 years 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