Bioconductor No replicates

Showing : no replicates • reset

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1.0k

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methylsig no replicates dmr

7.4 years ago nilaycan • 0

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3.9k

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deseq2 without replicate no replicates

updated 7.5 years ago by Michael Love 43k • written 7.5 years ago by Tony • 0

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12k

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deseq2 no replicates high p-adj values

updated 3.4 years ago by Michael Love 43k • written 8.2 years ago by Mahtetie • 0

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2.8k

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rnaseq edger DGE no replicates

8.3 years ago Stefany Solano • 0

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1.7k

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diffhic estimate dispersion value glm no replicates deseq

updated 8.7 years ago by Aaron Lun ★ 29k • written 8.7 years ago by hwick1 ▴ 20

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5.6k

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ATAC differential binding analysis no replicates DEseq2 chromatin

8.7 years ago BioinfGuru ▴ 70

6 results • Page 1 of 1

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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 …

Comment: problem reading bam files into nucleR by efoss ▴ 10

I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…

Answer: two questions about limma by Gordon Smyth 53k

Answered here: https://support.bioconductor.org/p/16318/

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

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Commentator to sina.nassiri ▴ 130