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Questions tagged [tximport]

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2 votes
2 answers
2k views

DESeqDataSetFromTximport all(lengths > 0) is not TRUE

I am suddenly running into an error when running the DESeqDataSetFromTximport ...
Julian's user avatar
  • 21
3 votes
1 answer
117 views

tximport txidcol and geneidcol selecting wrong column

I'm trying to run a differential expression analysis of 2 samples of the same species, but with different treatments using DESeq2. I'm using Ensembldb to create a tx2gene dataframe for tximport, ...
wolff's user avatar
  • 33
0 votes
2 answers
2k views

tx2gene file for tximport issue

I am trying to use tximport to get raw count matrices of a bulk RNA-seq sequencing experiment. I followed the tutorial: https://bioconductor.org/packages/3.7/bioc/...
Nikita Vlasenko's user avatar
2 votes
1 answer
520 views

Salmon tximport

I ran bulk RNA-seq experiment and got quant.sf file. Now, I am struggling with understanding what ...
Nikita Vlasenko's user avatar