Bioconductor Stringtie

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stringtie IsoformSwitchAnalyzeR pfamAnalyzeR gtf

updated 4 months ago by James W. MacDonald 65k • written 4 months ago by sumitra.20 • 0

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715

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DESeq2 TPM rawcounts StringTie

updated 20 months ago by Michael Love 41k • written 20 months ago by snijesh ▴ 20

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isoform RNA-seq hisat2 stringtie ballgown

3.6 years ago ra711 • 0

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ballgown StringTie galaxy rnaseq

updated 22 months ago by Kevin Blighe ★ 3.9k • written 3.7 years ago by lakshmi9c • 0

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deseq2 StringTie RNA-seq normalisation

updated 4.4 years ago by Michael Love 41k • written 4.4 years ago by JindrichK • 0

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featureCount rna-seq gene_id re_gene_id stringtie

updated 5.3 years ago by Wei Shi ★ 3.6k • written 5.3 years ago by IRAIA.MAIALEN • 0

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tximport stringtie RNA-seq analysis

updated 5.4 years ago by James W. MacDonald 65k • written 5.4 years ago by Mithil Gaikwad • 0

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prepDE STRINGTIE deseq2

updated 5.6 years ago by Michael Love 41k • written 5.6 years ago by Nancy ▴ 10

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tximport stringtie

6.2 years ago • updated 6.0 years ago matrs ▴ 10

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hisat2 stringtie ballgown RNAseq

6.2 years ago • updated 6.0 years ago Nancy ▴ 10

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Ballgown Stringtie DEG rnaseq

6.0 years ago vharshavardhanan • 0

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ballgown biologicalreplicates technical replicates stringtie

updated 6.4 years ago by Alyssa Frazee ▴ 210 • written 7.1 years ago by linda.boshans • 0

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stringtie illumina hisat2 ballgown

updated 6.4 years ago by k.vitting.seerup ▴ 120 • written 6.4 years ago by amy16 • 0

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ballgown stringtie

updated 7.1 years ago by linda.boshans • 0 • written 8.1 years ago by bhawley1991 ▴ 10

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ballgown stringtie voom limma differential gene expression rnaseq

updated 7.6 years ago by Alyssa Frazee ▴ 210 • written 7.6 years ago by jcalis ▴ 10

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ballgown stringtie

updated 7.8 years ago by Jeff Leek ▴ 650 • written 7.8 years ago by alva.james • 0

16 results • Page 1 of 1

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Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k

Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …

Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0

Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…

Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k

IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…

Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k

This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…

Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0

I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…

Votes

C: null model and DEXSeqDataSet object in DEXSEQ

A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?

A: How to explain how DESeq2 works to someone with zero bioinformatics background?

Answer: Interpret plot from DiffBind

Answer: How to retrieve gene ontology GO class from gene list?

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