Bioconductor Salmon rna seq

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deseq2 salmon rna seq salmon

updated 6.1 years ago by Michael Love 43k • written 6.1 years ago by danalvoronov ▴ 10

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2.0k

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salmon rna seq deseq2

updated 6.2 years ago by Michael Love 43k • written 6.2 years ago by Bob • 0

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1.4k

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deseq2 gsea tpm rnaseq salmon rna seq

updated 6.2 years ago by Michael Love 43k • written 6.2 years ago by leo_CD • 0

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1.7k

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tximport salmon rna seq de novo

updated 6.3 years ago by James W. MacDonald 67k • written 6.3 years ago by RMRG ▴ 10

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2.1k

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drimseq stageR dtu salmon rna seq

updated 6.5 years ago by Koen Van den Berge ▴ 180 • written 6.5 years ago by fiona.dick91 ▴ 60

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1.0k

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salmon rna seq tximport ruv-seq deseq2

updated 6.7 years ago by Michael Love 43k • written 6.7 years ago by mad6kj • 0

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2.8k

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sleuth R salmon rna seq salmon

7.2 years ago Walter F. Baumann ▴ 10

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1.3k

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salmon rna seq

updated 7.2 years ago by Michael Love 43k • written 7.2 years ago by tanyabioinfo ▴ 20

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Comment: iam not able to do retrive data using GEOquery R package by James W. MacDonald 67k

Another alternative is to use the `GEOmetadb` package ([vignette here)][1], which will allow you to make queries to identify GEO datasets t…

Answer: iam not able to do retrive data using GEOquery R package by James W. MacDonald 67k

Before you try to use a function, you should read the help page to ensure that you are using the correct argument type. As an example, here…

Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu by James W. MacDonald 67k

It's not the version control in R/Bioconductor though. It's the version of the genome. OP used Ensembl build 113 to align and then noted th…

Comment: Why did PCA plots look exactly the same after adjusting for batch covariate in D by Quang ▴ 10

Also, Michael, when I used SVA in addition, so I have the `design = ~ Date_lysed + SV1 + condition_subset`, do I just set `mat_corrected <-…

Comment: Differential variability modelling with vst() expression by Michael Love 43k

See Gordon's reply below for an implementation you can use directly.

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Answer: Differential variability modelling with vst() expression

Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu

Answer: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu

Comment: Why did PCA plots look exactly the same after adjusting for batch covariate in D

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