Bioconductor StringTie

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547

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stringtie IsoformSwitchAnalyzeR pfamAnalyzeR gtf

updated 11 months ago by James W. MacDonald 67k • written 12 months ago by sumitra.20 • 0

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870

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DESeq2 TPM rawcounts StringTie

updated 2.2 years ago by Michael Love 42k • written 2.2 years ago by snijesh ▴ 200

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1.6k

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isoform RNA-seq hisat2 stringtie ballgown

4.1 years ago ra711 • 0

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1.8k

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ballgown StringTie galaxy rnaseq

updated 2.4 years ago by Kevin Blighe ★ 4.0k • written 4.3 years ago by lakshmi9c • 0

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3.8k

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deseq2 StringTie RNA-seq normalisation

updated 4.9 years ago by Michael Love 42k • written 4.9 years ago by JindrichK • 0

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2.2k

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featureCount rna-seq gene_id re_gene_id stringtie

updated 5.8 years ago by Wei Shi ★ 3.6k • written 5.8 years ago by IRAIA.MAIALEN • 0

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1.5k

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tximport stringtie RNA-seq analysis

updated 6.0 years ago by James W. MacDonald 67k • written 6.0 years ago by Mithil Gaikwad • 0

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4.8k

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prepDE STRINGTIE deseq2

updated 6.1 years ago by Michael Love 42k • written 6.1 years ago by Nancy ▴ 10

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1.8k

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tximport stringtie

6.7 years ago • updated 6.5 years ago matrs ▴ 10

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2.1k

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hisat2 stringtie ballgown RNAseq

6.8 years ago • updated 6.5 years ago Nancy ▴ 10

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1.5k

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Ballgown Stringtie DEG rnaseq

6.5 years ago vharshavardhanan • 0

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2.8k

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ballgown biologicalreplicates technical replicates stringtie

updated 7.0 years ago by Alyssa Frazee ▴ 210 • written 7.7 years ago by linda.boshans • 0

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1.6k

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stringtie illumina hisat2 ballgown

updated 7.0 years ago by k.vitting.seerup ▴ 120 • written 7.0 years ago by amy16 • 0

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6.1k

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ballgown stringtie

updated 7.7 years ago by linda.boshans • 0 • written 8.7 years ago by bhawley1991 ▴ 10

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1.6k

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ballgown stringtie voom limma differential gene expression rnaseq

updated 8.2 years ago by Alyssa Frazee ▴ 210 • written 8.2 years ago by jcalis ▴ 10

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2.0k

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ballgown stringtie

updated 8.4 years ago by Jeff Leek ▴ 650 • written 8.4 years ago by alva.james • 0

16 results • Page 1 of 1

Recent ...

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Comment: ANOVA like approach of edgeR by Yunshun Chen ▴ 870

If you do it this way, the dispersion estimates would be much higher than they should (as the cell type difference is not accounted for in …

Comment: ANOVA like approach of edgeR by SamGG ▴ 350

Simply remove the cell type from the model. design <- model.matrix(~targets$Status)

Answer: ANOVA like approach of edgeR by Yunshun Chen ▴ 870

You could try the followings: > design <- model.matrix(~ 0 + group) > contrast <- makeContrasts(PvsL = 0.5*(L.pregnant + B.pregnan…

Answer: Identical samples after deseq2 batch effect removal by maripane • 0

Thanks Michael, so is there a way to work around this issue? Can I somehow make sure I can remove this batch effects without overcorrecti…

Comment: CleanUpRNAseq with a GTF that is missing mitochondria annotation data by rcreed • 0

The updated version worked well on my data. Thank you!

Votes

A: ANOVA-like test with edgeR

Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data

A: TopGO: How to retrieve the gene list related to a GO ID ?

A: Error in DESeqDataSet : some values in assay are not integers

Awards • All

Scholar to Haibo Liu ▴ 20