User: prab4th

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prab4th0
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Posts by prab4th

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Comment: C: How to create tx2gene data.frame when there's no TxDb object for the organism yo
... Hi, is there any reason you used kallisto over Salmon? ...
written 6 months ago by prab4th0
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Comment: C: How to get an output from DESeq2 to be used in WGCNA package
... Thank you! [Variance Stabilizing Transformation](https://www.rdocumentation.org/packages/DESeq/versions/1.24.0/topics/varianceStabilizingTransformation) at this link helped. I was surprised when l saw your name. ...
written 8 months ago by prab4th0
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How to get an output from DESeq2 to be used in WGCNA package
... Hello, I have a multiple time series RNA Sequencing data from this dataset https://trace.ddbj.nig.ac.jp/DRASearch/experiment?acc=ERX240756. And I want to format that data to be run in WGCNA as per instructions given here. https://wikis.utexas.edu/display/bioiteam/Clustering+using+WGCNA. It requires ...
deseq2 wgcna written 8 months ago by prab4th0 • updated 8 months ago by Peter Langfelder1.5k
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Comment: C: How to create tx2gene data.frame when there's no TxDb object for the organism yo
... Hello, This worked! thank you :) If you post your answer as a top level comment I can accept it.   Alsolibrary(GenomicFeatures) should be there for makeTxDbFromBiomart() to work. ...
written 8 months ago by prab4th0
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Comment: C: How to create tx2gene data.frame when there's no TxDb object for the organism yo
... These were the files availble for Oryza sativa: ftp://ftp.ensemblgenomes.org/pub/plants/release-37/gff3/oryza_sativa/ File: Oryza_sativa.IRGSP-1.0.37.gff3.gz File: Oryza_sativa.IRGSP-1.0.37.chr.gff3.gz File: Oryza_sativa.IRGSP-1.0.37.abinitio.gff3.gz File: Oryza_sativa.IRGSP-1.0.37.chromosome.1.gff ...
written 8 months ago by prab4th0
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Comment: C: How to create tx2gene data.frame when there's no TxDb object for the organism yo
... I'll try the `makeTxDbFromGff` first and get back to you if l couldn't get it to work. Thanks Jo   ...
written 9 months ago by prab4th0
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How to create tx2gene data.frame when there's no TxDb object for the organism you are working with.
... I have been following the workflow available at [Importing transcript abundance datasets with tximport](http://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html) and it is required to use a TxDb object. I am working with Rice and there isn't a TxDb object for rice. But ...
annotationdbi deseq2 tximport written 9 months ago by prab4th0 • updated 9 months ago by Johannes Rainer1.3k

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