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 9 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 9 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 9 months ago by Yunlu Zhu0 • updated 9 months ago by Michael Love20k

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