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

Dear all, I am happy to announce that {geneviewer*}* v0.1.10 is now on CRAN. *{geneviewer}* is an R package for plotting gene clusters and transcripts. It imports data from GenBank, FASTA, and GFF files, performs BlastP and MUMmer alignments, and displays results on gene arrow maps. The package offers extensive customization options, including legends, labels, annotations, scales, colors, tooltips, and more. - *CRAN:* https://cran.r-project.org/web/packages/geneviewer/index.html - *Gi...

Dear all, I am happy to announce that {geneviewer*}* v0.1.10 is now on CRAN. *{geneviewer}* is an R package for plotting gene clusters and transcripts. It imports data from GenBank, FASTA, and GFF files, performs BlastP and MUMmer alignments, and displays results on gene arrow maps. The package offers extensive customization options, including legends, labels, annotations, scales, colors, tooltips, and more. - *CRAN:* https://cran.r-project.org/web/packages/geneviewer/index.html - *Gi...

...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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