COHCAP Analysis of CpG Island Methylation for Illumina 450k Methylation Arrays
This protocol provides detailed instructions on how to produce quality control metrics, differentially methylated CpG sites, and differentially methylated CpG islands for Illumina 450k methylation array data using the COHCAP Bioconductor package. Scripts for comparing tools to identify differentially methylated regions are also provided, with benchmarks described in the introduction to this protocol.
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COHCAP is now available as a release package:http://bioconductor.org/packages/release/bioc/html/COHCAP.htmlSo, you can now use the standard Bioconductor installation procedure to install COHCAP. Just make sure you are using R-3.1.0 or later (earlier versions of R won't work with Bioconductor 2.14, which is necessary to access the release version of COHCAP).
I have recently learned about this more broad 450k tutorial: https://www.biostars.org/p/110887/Also, these scripts may be worth checking out (but I haven't tried them myself): https://www.biostars.org/p/54994/
I had to list one group, and COHCAP was originally developed when I was working in the Bioinformatics Core; however, I was actually working in the Integrative Genomics Core when I created the Bioconductor version. That is why I have added Xiwei Wu as an author on the Bioconductor page.
COHCAP is now available as a release package:http://bioconductor.org/packages/release/bioc/html/COHCAP.htmlSo, you can now use the standard Bioconductor installation procedure to install COHCAP. Just make sure you are using R-3.1.0 or later (earlier versions of R won't work with Bioconductor 2.14, which is necessary to access the release version of COHCAP).
I have recently learned about this more broad 450k tutorial: https://www.biostars.org/p/110887/Also, these scripts may be worth checking out (but I haven't tried them myself): https://www.biostars.org/p/54994/
Posted 30 Jan, 2014
COHCAP Analysis of CpG Island Methylation for Illumina 450k Methylation Arrays
Posted 30 Jan, 2014
This protocol provides detailed instructions on how to produce quality control metrics, differentially methylated CpG sites, and differentially methylated CpG islands for Illumina 450k methylation array data using the COHCAP Bioconductor package. Scripts for comparing tools to identify differentially methylated regions are also provided, with benchmarks described in the introduction to this protocol.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8
Figure 9
Figure 10
COHCAP is now available as a release package:http://bioconductor.org/packages/release/bioc/html/COHCAP.htmlSo, you can now use the standard Bioconductor installation procedure to install COHCAP. Just make sure you are using R-3.1.0 or later (earlier versions of R won't work with Bioconductor 2.14, which is necessary to access the release version of COHCAP).
I have recently learned about this more broad 450k tutorial: https://www.biostars.org/p/110887/Also, these scripts may be worth checking out (but I haven't tried them myself): https://www.biostars.org/p/54994/
I had to list one group, and COHCAP was originally developed when I was working in the Bioinformatics Core; however, I was actually working in the Integrative Genomics Core when I created the Bioconductor version. That is why I have added Xiwei Wu as an author on the Bioconductor page.
COHCAP is now available as a release package:http://bioconductor.org/packages/release/bioc/html/COHCAP.htmlSo, you can now use the standard Bioconductor installation procedure to install COHCAP. Just make sure you are using R-3.1.0 or later (earlier versions of R won't work with Bioconductor 2.14, which is necessary to access the release version of COHCAP).
I have recently learned about this more broad 450k tutorial: https://www.biostars.org/p/110887/Also, these scripts may be worth checking out (but I haven't tried them myself): https://www.biostars.org/p/54994/
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