Bioconductor StringTie

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344

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stringtie IsoformSwitchAnalyzeR pfamAnalyzeR gtf

updated 6 months ago by James W. MacDonald 66k • written 6 months ago by sumitra.20 • 0

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748

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DESeq2 TPM rawcounts StringTie

updated 21 months ago by Michael Love 42k • written 21 months ago by snijesh ▴ 20

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1.4k

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isoform RNA-seq hisat2 stringtie ballgown

3.7 years ago ra711 • 0

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1.5k

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ballgown StringTie galaxy rnaseq

updated 24 months ago by Kevin Blighe ★ 3.9k • written 3.9 years ago by lakshmi9c • 0

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3.5k

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deseq2 StringTie RNA-seq normalisation

updated 4.5 years ago by Michael Love 42k • written 4.5 years ago by JindrichK • 0

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1.8k

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featureCount rna-seq gene_id re_gene_id stringtie

updated 5.4 years ago by Wei Shi ★ 3.6k • written 5.4 years ago by IRAIA.MAIALEN • 0

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1.4k

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tximport stringtie RNA-seq analysis

updated 5.6 years ago by James W. MacDonald 66k • written 5.6 years ago by Mithil Gaikwad • 0

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4.4k

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prepDE STRINGTIE deseq2

updated 5.7 years ago by Michael Love 42k • written 5.7 years ago by Nancy ▴ 10

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1.6k

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tximport stringtie

6.3 years ago • updated 6.1 years ago matrs ▴ 10

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1.9k

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hisat2 stringtie ballgown RNAseq

6.3 years ago • updated 6.1 years ago Nancy ▴ 10

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1.4k

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Ballgown Stringtie DEG rnaseq

6.1 years ago vharshavardhanan • 0

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2.6k

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ballgown biologicalreplicates technical replicates stringtie

updated 6.5 years ago by Alyssa Frazee ▴ 210 • written 7.3 years ago by linda.boshans • 0

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1.4k

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stringtie illumina hisat2 ballgown

updated 6.6 years ago by k.vitting.seerup ▴ 120 • written 6.6 years ago by amy16 • 0

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5.8k

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ballgown stringtie

updated 7.3 years ago by linda.boshans • 0 • written 8.3 years ago by bhawley1991 ▴ 10

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1.4k

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ballgown stringtie voom limma differential gene expression rnaseq

updated 7.7 years ago by Alyssa Frazee ▴ 210 • written 7.7 years ago by jcalis ▴ 10

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1.8k

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ballgown stringtie

updated 7.9 years ago by Jeff Leek ▴ 650 • written 7.9 years ago by alva.james • 0

16 results • Page 1 of 1

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Comment: error loading collectTRI regulon by silvaesilva.da • 0

Fantastic. Thank you very much. Everything has been sorted out

Answer: DESeq2 returns results for group with just one replicate by James W. MacDonald 66k

There is no problem having only one replicate per group, so long as you have replicates for other groups. The degrees of freedom are based …

Answer: Limma model.matrix design with batch effect and different life stages proportion by Masongeorge • 0

Thanks for this post. i found it helpful for my own issue that was occurring on the backend of this page.

Comment: error loading collectTRI regulon by deeenes ▴ 50

I fixed the original, Ensembl HTTP 403 error only now, [see here][1]. If you've seen it gone earlier today, only shows that this error appe…

Answer: GESA with certain gene list returns no result with human genom, but many result by James W. MacDonald 66k

Ideally you would use something better than gene symbols for this. I realize that biologists like gene symbols, but they are really terribl…

Votes

Answer: DESeq2 returns results for group with just one replicate

Comment: error loading collectTRI regulon

A: Scaling option in fastMNN

Answer: Behaviour of featureCounts when quantifying multi-mapping reads

Awards • All

Scholar to James W. MacDonald 66k