Hi everyone, I am in the process of analyzing a lot of ChIP-seq data and I am writing to ask if an analysis module becomes available for R/Bioconductor anytime soon. Any information would be greatly appreciated. Thanks and best regards. Bogdan

Hi Bodan -- "Bogdan Tanasa" <tanasa at="" gmail.com=""> writes: > Hi everyone, > > I am in the process of analyzing a lot of ChIP-seq data and I am writing to ask > if an analysis module becomes available for R/Bioconductor anytime soon. Visit the bioc-sig-sequencing news group (Cc'd in the reply) https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing Current packages include Biostrings (for lots of string matching / manipulation facilities) and ShortRead (for IO from ELAND or MAQ, for instance, plus additional sorting, counting, and qa-related functionality. There are posts in the bioc-sig-sequencing news group about package use. Maybe others will reply (to bioc-sig-sequencing) with additional developments; I know people are working with and developing packages for this data in R. Martin > Any information would be greatly appreciated. Thanks and best regards. > > Bogdan > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793

Hi Bodan -- "Bogdan Tanasa" <tanasa at="" gmail.com=""> writes: > Hi everyone, > > I am in the process of analyzing a lot of ChIP-seq data and I am writing to ask > if an analysis module becomes available for R/Bioconductor anytime soon. Visit the bioc-sig-sequencing news group (Cc'd in the reply) https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing Current packages include Biostrings (for lots of string matching / manipulation facilities) BSgenome (reference sequences, including masked and SNP-injected versions) and ShortRead (for IO from ELAND or MAQ, for instance, plus additional sorting, counting, and qa-related functionality. There are posts in the bioc-sig-sequencing news group about package use. Maybe others will reply (to bioc-sig-sequencing) with additional developments; I know people are working with and developing packages for this data in R. Martin > Any information would be greatly appreciated. Thanks and best regards. > > Bogdan > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793