Bioconductor Confounders

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scRNA-seq MAST confounders

updated 5.1 years ago by Andrew_McDavid ▴ 270 • written 5.1 years ago by ramonmassoni ▴ 10

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1.9k

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limma limma-voom limma design matrix confounders

updated 6.6 years ago by Aaron Lun ★ 28k • written 6.6 years ago by S.Bamopoulos ▴ 10

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1.2k

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deseq2 confounders nanostring rnaseq differential gene expression

updated 6.8 years ago by Michael Love 43k • written 6.8 years ago by kim.malek88 • 0

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2.5k

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ruvseq deseq2 model.matrix confounders

updated 7.5 years ago by davide risso ▴ 980 • written 7.5 years ago by heikki.sarin ▴ 10

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2.8k

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deseq2 confounders design matrix rnaseq

7.8 years ago lina.faller ▴ 10

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2.2k

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minfi bumphunter confounders

updated 7.8 years ago by James W. MacDonald 67k • written 7.8 years ago by gft219 • 0

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2.0k

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edgeR paired samples confounders model.matrix

updated 8.6 years ago by Ryan C. Thompson ★ 7.9k • written 8.6 years ago by manasishah86 ▴ 30

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5.0k

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deseq2 rnaseq_analysis variancestabilizingtransformation confounders

updated 8.7 years ago by Michael Love 43k • written 8.7 years ago by ompandey ▴ 10

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5.2k

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Deseq2 dds confounders

updated 9.1 years ago by Michael Love 43k • written 9.1 years ago by colaneri ▴ 30

9 results • Page 1 of 1

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Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k

FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…

Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10

I see. Thank you ATpoint!

Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0

Thanks James!

Comment: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k

I think I explained what the differences between approach 1 and 2 is in my answer. I assume that the tutorial uses vst because it is varian…

Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10

Thank you ATpoint for your responses. I am a bit confused because the difference between the two approaches is the selection of the genes…

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A: PDCD1 missing from TxDb.Hsapiens.UCSC.hg38.knownGene?

PDCD1 missing from TxDb.Hsapiens.UCSC.hg38.knownGene?

Bioconductor Course, Kenya 2025: Applications Open!

Comment: can't install tscR

Answer: Csaw normalization strategies - general inquiry

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