GenePattern Team Blog

End of support for Cufflinks suite of modules

Posted on Thursday, October 28, 2021 at 01:52PM by Barbara Hill

The Cufflinks suite of modules is no longer under active development and is therefore deprecated. 

The Cufflinks suite of modules includes:

  • Cufflinks
  • Cuffcompare
  • Cuffmerge
  • Cuffdiff
  • CufflinksCuffmergePipeline (and the CufflinksWrapperPipeline)

It is no longer available on any of our servers or module repositories.

The module zip files and documentation are now archived in GitHub.

Please contact us if you have any questions.

 

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End of support for MAGeCK

Posted on Thursday, October 14, 2021 at 05:53PM by Barbara A Hill

MAGeCK is no longer supported by the original author and is therefore deprecated. 

It is no longer available on any of our servers or module repositories.

The source repositories are now archived in GitHub.

Please contact us if you have any questions.

 

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End of Support for the PathSeq pipeline and associated modules

Posted on Thursday, March 25, 2021 at 07:33PM by Barbara A Hill

Due to the end of support for the PathSeq pipeline and its modules by the authors, we have had to end support for the PathSeq pipeline in GenePattern. This means the PathSeq pipeline and its associated modules (see below) are no longer installed on any of our servers and are no longer available from any of our repositories. This includes the following:

  • BlastNPipeline
  • BlastParser
  • BlastSubtraction
  • BlastSubtractionLoop
  • BlastXml
  • BWA.Unmapped
  • BWAPipeline
  • BWASubtraction
  • CatalogueReads
  • ConcatenateFiles
  • ExternalSort
  • ExtractFullQuery
  • ExtractPairsBam
  • ExtractUnmapped
  • ExtractUnmappedAdapterBlast
  • Fasta2FQone
  • Fastq2FQone
  • FilterLength
  • FQone2Fasta
  • FQone2Fastq
  • GetUnmappedReads
  • MegaBlastPipeline
  • ParsedBlastParser
  • PathSeq.BlastN
  • PathSeq.BlastX 
  • PathSeq.BWA.aln
  • PathSeq.MegaBlast 
  • PathSeqPrototype
  • PathseqReport 
  • PostBlastN.All
  • PostBlastX.All
  • PostMegaBlast.Bacterial 
  • PostMegaBlast.Ribosomal 
  • PostSubtraction 
  • PostSubtraction.Assembly
  • PostSubtraction.Contigs
  • ...

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