Bioconductor Rrbs

Showing : rrbs • reset

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1.6k

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edgeR model-selection RRBS mixture-experiment

4.7 years ago ingerslev • 0

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1.3k

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MethylCC RRBS cord blood

5.4 years ago weichen-cls • 0

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1.1k

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Biseq Methylation DMP DMR RRBS

5.4 years ago i.s.castanho • 0

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991

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biseq betaRegression RRBS Methylation

5.7 years ago i.s.castanho • 0

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3.0k

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edgeR rrbs

updated 6.9 years ago by Gordon Smyth 53k • written 6.9 years ago by ingerslev • 0

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3.3k

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methykit rrbs

updated 7.6 years ago by Mike Smith ★ 6.6k • written 7.6 years ago by bekah ▴ 40

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2.1k

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edgeR methyation RRBS

updated 7.9 years ago by Gordon Smyth 53k • written 7.9 years ago by osa.zuta ▴ 40

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1.5k

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biseq RRBS betaregression

8.7 years ago l.eijssen • 0

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2.6k

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sva RRBS

updated 8.7 years ago by Jeff Leek ▴ 650 • written 8.7 years ago by mrodrigues.fernanda ▴ 10

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2.2k

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rrbs batch effect methylation sva

updated 9.2 years ago by dashbrook1 • 0 • written 10.4 years ago by GFM ▴ 20

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1.9k

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limma rrbs bsseq

updated 9.5 years ago by Aaron Lun ★ 29k • written 9.5 years ago by nhejazi • 0

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2.7k

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biseq RRBS SAAP-BS coverage

10.6 years ago maria.maqueda • 0

12 results • Page 1 of 1

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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 …

Votes

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