User: Yunlu Zhu

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Yunlu Zhu0
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Posts by Yunlu Zhu

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Comment: C: If transcript-to-gene conversion is needed in kallisto > tximport > DESeq2 pipel
... I'll just use tximport (txOut = FALSE and tx2gene) to estimate abundance at gene level, then proceed to the DESeq2 and following analysis. Thank you very much Mike! This is very helpful! ...
written 12 months ago by Yunlu Zhu0
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Comment: C: If transcript-to-gene conversion is needed in kallisto > tximport > DESeq2 pipel
... Yes, the DE analysis seems to work well. but for gene ontology and pathway-level analysis, is it necessary to generate a gene-level dds? Thanks! ...
written 12 months ago by Yunlu Zhu0
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If transcript-to-gene conversion is needed in kallisto > tximport > DESeq2 pipeline
... Hi guys,  I'm new to bioinformatics so this may be a naive question. My workflow: 1.  tximport function to create the txi data frame from .h5 kallisto files 2.  DESeqDataSetFromTximport function to generate DESeq data set Question: Do I need to generate gene-level unnormalized counts during the ...
rnaseq deseq2 tximport kallisto written 12 months ago by Yunlu Zhu0 • updated 12 months ago by Michael Love22k

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