Bioconductor Stringtie

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5.7k

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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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4.3k

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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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3.4k

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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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2.5k

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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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1.8k

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hisat2 stringtie ballgown RNAseq

6.2 years ago • updated 6.0 years ago Nancy ▴ 10

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1.8k

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ballgown stringtie

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

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1.7k

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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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1.5k

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tximport stringtie

6.2 years ago • updated 6.0 years ago matrs ▴ 10

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1.4k

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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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1.4k

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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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1.4k

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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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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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Ballgown Stringtie DEG rnaseq

6.0 years ago vharshavardhanan • 0

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1.3k

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isoform RNA-seq hisat2 stringtie ballgown

3.6 years ago ra711 • 0

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716

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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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268

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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

16 results • Page 1 of 1

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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0

Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…

Comment: PCA plot suggestions by JKim • 0

cross post: https://www.biostars.org/p/9593486/

Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k

You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…

Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k

You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…

Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0

My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…

Votes

Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2

Answer: Use of negative binomial model for exponential decay rate estimation using DESeq

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?

Awards • All

Scholar to James W. MacDonald 65k

Supporter to JKim • 0