Bioconductor Svaseq

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937

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DESeq2 Normalisation Bulkrnaseq Svaseq

18 months ago BioinfGuru ▴ 70

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1.1k

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RUVSeq svaseq

3.4 years ago Tongjun • 0

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RNASeq sva svaseq

updated 3.9 years ago by James W. MacDonald 68k • written 3.9 years ago by Bex • 0

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limma sva Leafcutter SVAseq

4.2 years ago georgia.katsoula ▴ 40

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1.2k

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sva svaseq surrogate variable analysis

updated 5.6 years ago by James W. MacDonald 68k • written 5.6 years ago by Mozart ▴ 30

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svaseq sva

6.7 years ago flippy23 • 0

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1.2k

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MEDIPS svaseq sva

updated 6.9 years ago by Lukas Chavez ▴ 570 • written 6.9 years ago by tofukaj • 0

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deseq2 svaseq

6.9 years ago bioinfo • 0

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2.1k

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edger sva svaseq limma

updated 7.5 years ago by Ryan C. Thompson ★ 7.9k • written 7.5 years ago by cats_dogs ▴ 20

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DESeq2 sva svaseq batch effect correction

7.9 years ago L_K • 0

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1.5k

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svaseq batcheffectcorrection

8.1 years ago burcu.atasu • 0

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2.0k

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ruvseq svaseq edaseq

updated 8.1 years ago by davide risso ▴ 980 • written 8.1 years ago by llo ▴ 10

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1.6k

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sva svaseq batch effect batch effects batch effect correction

8.3 years ago vedran.franke • 0

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2.2k

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deseq2 svaseq

updated 8.3 years ago by Michael Love 43k • written 8.3 years ago by gpalidwor ▴ 10

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sva svaseq

updated 8.5 years ago by Guido Hooiveld ★ 4.1k • written 8.5 years ago by wamiqsaifi • 0

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limma sva svaseq

updated 8.8 years ago by Aaron Lun ★ 29k • written 8.8 years ago by Bogdan ▴ 670

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2.3k

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svaseq dexseq

updated 8.8 years ago by Alejandro Reyes ★ 1.9k • written 8.8 years ago by tofukaj • 0

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svaseq combat sva RANseq batcheffect removebatcheffect

updated 9.1 years ago by Jakub ▴ 50 • written 9.1 years ago by amoltej ▴ 10

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deseq2 svaseq

9.2 years ago Akula, Nirmala NIH/NIMH [C] ▴ 190

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2.4k

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deseq2 sva svaseq

updated 9.3 years ago by Michael Love 43k • written 9.3 years ago by szenitha ▴ 20

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3.1k

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sva svaseq batcheffectcorrection

updated 9.3 years ago by Jeff Leek ▴ 650 • written 9.3 years ago by szenitha ▴ 20

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4.4k

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deseq2 sva svaseq pca

9.5 years ago Peter Alto ▴ 20

22 results • Page 1 of 1

Recent ...

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Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k

BTW, I tested with no issue on MacOS ARM on our previous github issue.

Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k

The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…

Answer: PTM analysis in LIMPA by Gordon Smyth 53k

For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…

Answer: problem reading bam files into nucleR by James W. MacDonald 68k

The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…

Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k

It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …

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C: DESeq2 Following RSEM

Upcoming Ensembl API and data access changes - new blog post available

Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?

Answer: Large logFC but somewhat high FDR

Comment: upstream git branches of bioc-release

Awards • All

Commentator to sina.nassiri ▴ 130