User: prab4th

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prab4th0
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Posts by prab4th

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Comment: C: How to get an output from DESeq2 to be used in WGCNA package
... Did you hear back from him? ...
written 13 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
... Hi, is there any reason you used kallisto over Salmon? ...
written 2.0 years 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 2.2 years 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 2.2 years ago by prab4th0 • updated 2.2 years ago by Peter Langfelder2.3k
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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 2.2 years 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 2.2 years 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 2.2 years 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 2.2 years ago by prab4th0 • updated 2.2 years ago by Johannes Rainer1.5k

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