search for: gff

Hi All I am wondering if people based on their experience could share what methods one could use to compare two gff/gtf files. The reason why I want to do so is that we have constructed a RNA-Seq based transcriptome and would like to compare it with reference transcriptome we had from in-silico approaches. Ideally we are looking to find out 1. new genes we see 2. transcripts where the start/end side is change...

...following information is mainly for developers, package maintainers and repository maintainers. The planned procedure is Sep 5: "Grand Feature" Freeze 2.6.0 alpha Sep 19: Feature Freeze 2.6.0 beta Sep 26: Code Freeze 2.6.0 RC Oct 3: Release 2.6.0 GFF: No major restructuring past this point FF: Feature set complete, only bugfixing from now on CF: Only critical bugfixes and platform build issues Maintainers of recommended packages should notice that as they become part of the final R tarball, we expect them to follow a similar freeze pattern (...

...information is mainly for developers, package maintainers and repository maintainers. The planned procedure is March 27: "Grand Feature" Freeze 2.5.0 alpha April 10: Feature Freeze 2.5.0 beta April 17: Code Freeze 2.5.0 RC April 24: Release 2.5.0 GFF: No major restructuring past this point FF: Feature set complete, only bugfixing from now on CF: Only critical bugfixes and platform build issues Maintainers of recommended packages should notice that as they become part of the final R tarball, we expect them to follow a similar freeze pattern (...

...following information is mainly for developers, package maintainers and repository maintainers. The planned procedure is Mar 25: "Grand Feature" Freeze 2.7.0 alpha Apr 8: Feature Freeze 2.7.0 beta Apr 15: Code Freeze 2.7.0 RC Apr 22: Release 2.7.0 GFF: No major restructuring past this point FF: Feature set complete, only bugfixing from now on CF: Only critical bugfixes and platform build issues Maintainers of recommended packages should notice that as they become part of the final R tarball, we expect them to follow a similar freeze pattern (...

Dear guangchuang, I was stopped by the following error when using Package: clusterProfiler on R 2.15.3 on windows 7. Error in xzfile(file, “wb”, compression = 9) : Cannot open the connection In addition: warning message: cannot initialize lzma encoder, error 5 The too functions: Gff2GeneTable() and buildGOmap() are not working because of this error. Could you please let me know how to fix these error. [source of the package: http://bioconductor.org/packages/2.11/bioc/html/clusterProfiler.html] Here are what I typed in R: ----------------------------------------------------...

Hi all: I got basic rsync working (not server mode). Basically it went to another server via ssh, backed up subdireactories and stored on the local server. But I am trying to use the feature of "exclude" and could not get it working rigjt. I am trying to back up /export/home/* (all of users) on another machine but exclude a certain types of files. here is one of my tested exclude

...V1 V2 V3 1 foom 0 0 2 bar 0 0 while until now and on 2.6.2 > tab <- read.table("test.txt",as.is=TRUE) > tab V1 V2 V3 1 foom + . 2 bar - . the really strange thing I just saw when preparing the simplified test case - I normally use tab delimited files (biological gff files by the way where +/- and . have some meaning). on 2.7.0: tab <- read.table("test.txt",sep="\t", as.is=TRUE) > tab V1 1 foom + . 2 bar - . so specifying the wrong separator brings up the old correct behaviour. best wishes, ido PS: I hope I cancelled the f...

Great R people, I have noticed a strange behaviour in read.delim() and friends in the R 2.7.0 version. I will describe you the problem and also the solution I already found, just to be sure it is an expected behaviour and also to tell people, who may experience the same difficulty, a way to overcome it. And also to see if it is a proper behaviour or maybe a correction is needed. Here is the

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