Bioconductor Stringtie

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DESeq2 TPM rawcounts StringTie

updated 13 months ago by Michael Love 40k • written 13 months ago by snijesh ▴ 20

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isoform RNA-seq hisat2 stringtie ballgown

3.0 years ago ra711 • 0

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ballgown StringTie galaxy rnaseq

updated 15 months ago by Kevin Blighe 3.8k • written 3.2 years ago by lakshmi9c • 0

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deseq2 StringTie RNA-seq normalisation

updated 3.8 years ago by Michael Love 40k • written 3.8 years ago by JindrichK • 0

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1.4k

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featureCount rna-seq gene_id re_gene_id stringtie

updated 4.7 years ago by Wei Shi ★ 3.5k • written 4.7 years ago by IRAIA.MAIALEN • 0

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1.1k

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tximport stringtie RNA-seq analysis

updated 4.9 years ago by James W. MacDonald 63k • written 4.9 years ago by Mithil Gaikwad • 0

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3.8k

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prepDE STRINGTIE deseq2

updated 5.0 years ago by Michael Love 40k • written 5.0 years ago by Nancy ▴ 10

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1.3k

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tximport stringtie

5.6 years ago • updated 5.4 years ago matrs ▴ 10

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hisat2 stringtie ballgown RNAseq

5.6 years ago • updated 5.4 years ago Nancy ▴ 10

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1.1k

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Ballgown Stringtie DEG rnaseq

5.4 years ago vharshavardhanan • 0

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ballgown biologicalreplicates technical replicates stringtie

updated 5.8 years ago by Alyssa Frazee ▴ 210 • written 6.6 years ago by linda.boshans • 0

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1.1k

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stringtie illumina hisat2 ballgown

updated 5.9 years ago by k.vitting.seerup ▴ 120 • written 5.9 years ago by amy16 • 0

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ballgown stringtie

updated 6.6 years ago by linda.boshans • 0 • written 7.6 years ago by bhawley1991 ▴ 10

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ballgown stringtie voom limma differential gene expression rnaseq

updated 7.0 years ago by Alyssa Frazee ▴ 210 • written 7.0 years ago by jcalis ▴ 10

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1.6k

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ballgown stringtie

updated 7.2 years ago by Jeff Leek ▴ 640 • written 7.2 years ago by alva.james • 0

15 results • Page 1 of 1

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Answer: Batch effect adjust in model matrix by ATpoint ★ 3.4k

Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k

Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0

I´m sorry causing confusion here, but the gene matrices I refer to are actually obtained via https://nf-co.re/rnaseq. The problem with the…

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k

For the reasons outlined in the Soneson paper, I'd prefer this pipeline: https://nf-co.re/rnaseq You cannot use these scaled TPM approach…

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0

I get your point as we already starting with TPM. This was more to clarify that I understand the principle correctly. However, further I´m…

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batch effect : comBat or blocking in limma ?

Batch correction and repeated measures

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?

Comment: Phenotype effect - building a contrast matrix - grouping vs interaction

Answer: Batch correction and repeated measures

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