Re: [Bioc-devel] big file ReactomeFI --> bioC annotate package

There are helper functions in GenomicFeatures to make TxDbs from various types of data: library(GenomicFeatures) > makeTxDb makeTxDbmakeTxDbFromGFF makeTxDbFromUCSCmakeTxDbPackageFromBiomart makeTxDbFromBiomart makeTxDbFromGRanges

Re: [Bioc-devel] big file ReactomeFI --> bioC annotate package

Thank you Valerie, TxDb uses sqlite format. Maybe I need to know how to convert reactomeFI.txt to reactomeFI.sqlite. I found frombioC workshop 2006 a Lab: How to use SQLite . Is it a

Re: [Bioc-devel] big file ReactomeFI --> bioC annotate package

Hi Karim, I can help you put together an annotation package. Here are the general guidelines: http://www.bioconductor.org/developers/package-guidelines/ We ask that annotations packages implement the select() interface from AnnotationDbi (eg, keys(), columns(), keytypes(), etc.). You can see

[Bioc-devel] big file ReactomeFI --> bioC annotate package

Dear bioC developer, I included in my bioCancer/inst/extdata a Reactome FI database (/ http://reactomews.oicr.on.ca:8080/caBigR3WebApp2015/FIsInGene_031516_with_annotations.txt.zip ) Gene1Gene2AnnotationDirectionScore 16-5-5CDC42predicted-0.82 16-5-5RHOJ