Bioconductor Confounders

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scRNA-seq MAST confounders

updated 3.7 years ago by Andrew_McDavid ▴ 270 • written 3.7 years ago by ramonmassoni ▴ 10

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1.5k

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limma limma-voom limma design matrix confounders

updated 5.3 years ago by Aaron Lun ★ 28k • written 5.3 years ago by S.Bamopoulos ▴ 10

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947

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deseq2 confounders nanostring rnaseq differential gene expression

updated 5.5 years ago by Michael Love 40k • written 5.5 years ago by kim.malek88 • 0

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1.9k

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ruvseq deseq2 model.matrix confounders

updated 6.1 years ago by davide risso ▴ 920 • written 6.1 years ago by heikki.sarin ▴ 10

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2.0k

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deseq2 confounders design matrix rnaseq

6.4 years ago lina.faller • 0

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1.6k

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minfi bumphunter confounders

updated 6.5 years ago by James W. MacDonald 63k • written 6.5 years ago by gft219 • 0

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1.5k

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edgeR paired samples confounders model.matrix

updated 7.2 years ago by Ryan C. Thompson 7.8k • written 7.2 years ago by manasishah86 ▴ 30

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3.8k

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deseq2 rnaseq_analysis variancestabilizingtransformation confounders

updated 7.3 years ago by Michael Love 40k • written 7.3 years ago by ompandey ▴ 10

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4.3k

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Deseq2 dds confounders

updated 7.8 years ago by Michael Love 40k • written 7.8 years ago by colaneri ▴ 30

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Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k

> I don't know the details but do you mean using HDF5RealizationSink or TENxRealizationSink will make it possible to writing sparse multi-d…

Comment: DMRcate design by Jitendra ▴ 10

Thanks James, do I also need to mention 'contrasts=FALSE' in cpg.annotate.And also what to mentions in analysis.type="differential",/ "ANO…

Comment: Speeding up of DelayedArray::write_block() by Koki ▴ 10

I don't know the details but do you mean using `HDF5RealizationSink` or `TENxRealizationSink` will make it possible to writing sparse multi…

Comment: DelayedArray::read_sparse_block by Koki ▴ 10

Ok, I understood. How about "writing" to HDF5? Are you going to implement `write_block_as_sparse` in `SparseArray` package?

Comment: DelayedArray::read_sparse_block by Hervé Pagès 16k

> So do you means the specification change from DelayedArray's read_sparse_block to SparseArray's read_block_as_sparse will accelerate the …

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Steps needed to change design (relevel factors) in DESeq2

Answer: DMRcate design

Comment: DMRcate design

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