Bioconductor ScRna-Seq

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2.3k

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DropletUtils scRNA-seq emptyDrops simplesinglecell cell calling

updated 4.1 years ago by Aaron Lun ★ 28k • written 5.2 years ago by C T ▴ 140

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1.6k

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deseq2 zinbwave 10X scRNA-seq Differential expression

updated 4.4 years ago by Michael Love 42k • written 4.4 years ago by vincent.croset ▴ 20

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3.5k

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cmdscale zinbwave scRNA-seq single cell sequencing RNA-seq

updated 4.4 years ago by davide risso ▴ 980 • written 4.4 years ago by Wagaa ▴ 10

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818

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scRNA-seq time series

4.4 years ago Bogdan ▴ 670

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1.1k

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assayData() scRNA-seq single cell sequencing assayData Bioconductor

updated 4.5 years ago by Kevin Blighe ★ 4.0k • written 4.5 years ago by Wagaa ▴ 10

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3.4k

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mnn batchelor scrna-seq seurat

updated 4.5 years ago by Aaron Lun ★ 28k • written 4.5 years ago by heir_of_isildur88 • 0

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6.4k

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scrna-seq downsampleBatches scran

updated 4.6 years ago by Aaron Lun ★ 28k • written 4.6 years ago by p.joshi ▴ 40

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2.2k

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RNA-seq scRNA-seq

updated 4.8 years ago by Aaron Lun ★ 28k • written 4.8 years ago by Bogdan ▴ 670

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1.8k

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scrna-seq integration batch correction

updated 4.8 years ago by Aaron Lun ★ 28k • written 4.9 years ago by p.joshi ▴ 40

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2.0k

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batchelor mnn scrna-seq

updated 2.3 years ago by Guandong Shang ▴ 40 • written 4.9 years ago by heir_of_isildur88 • 0

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890

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scRNA-seq

updated 4.9 years ago by Aaron Lun ★ 28k • written 4.9 years ago by Bogdan ▴ 670

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1.6k

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scRNA-seq MAST confounders

updated 4.9 years ago by Andrew_McDavid ▴ 270 • written 4.9 years ago by ramonmassoni ▴ 10

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1.1k

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scRNA-seq CNS transcriptomics RNAi Job

4.9 years ago Joseph Barry ▴ 10

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2.3k

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scRNA-Seq scater scran rna-seq MNN

updated 5.1 years ago by Aaron Lun ★ 28k • written 5.1 years ago by hamza_karakurt ▴ 60

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3.0k

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scRNA-seq Seurat DE

updated 5.2 years ago by Aaron Lun ★ 28k • written 5.2 years ago by ilee8 • 0

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1.0k

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scran dropletUtils scater scRNA-Seq

5.5 years ago hamza_karakurt ▴ 60

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2.5k

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edger scRNA-seq DGEA

updated 5.6 years ago by Aaron Lun ★ 28k • written 5.6 years ago by cronanz • 0

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2.9k

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10x scrna-seq

updated 5.6 years ago by Aaron Lun ★ 28k • written 5.6 years ago by jma1991 ▴ 70

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3.0k

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scater scran scRNA-Seq doubletCells

updated 5.6 years ago by Aaron Lun ★ 28k • written 5.6 years ago by hamza_karakurt ▴ 60

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2.1k

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SC3 Scater Scran scRNA-Seq Batch Correction

updated 5.6 years ago by Vladimir Kiselev ▴ 150 • written 5.6 years ago by hamza_karakurt ▴ 60

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1.7k

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scRNA-Seq clustering scater scran dunn index

updated 5.7 years ago by Aaron Lun ★ 28k • written 5.7 years ago by hamza_karakurt ▴ 60

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6.9k

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deseq2 scRNA-Seq RNA-Seq differential expression analysis

updated 5.7 years ago by Michael Love 42k • written 5.7 years ago by hamza_karakurt ▴ 60

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1.8k

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scater scran igraph scRNA-Seq rots

updated 5.7 years ago by Aaron Lun ★ 28k • written 5.7 years ago by hamza_karakurt ▴ 60

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2.0k

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R GSEA rna-seq scRna-Seq

updated 5.7 years ago by Peter Langfelder ★ 3.0k • written 5.7 years ago by hamza_karakurt ▴ 60

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4.5k

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scran scater Rtsne ggplot2 scRNA-Seq

updated 2.2 years ago by jamie.gearing ▴ 60 • written 5.8 years ago by hamza_karakurt ▴ 60

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2.7k

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scRNA-Seq RNA-Seq Clustering Silhouette Plot

updated 5.8 years ago by Aaron Lun ★ 28k • written 5.8 years ago by hamza_karakurt ▴ 60

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1.7k

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scRNA-seq

updated 5.9 years ago by James W. MacDonald 67k • written 5.9 years ago by Bogdan ▴ 670

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1.5k

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scRNA-seq seurat CCA

updated 5.9 years ago by Aaron Lun ★ 28k • written 5.9 years ago by Bogdan ▴ 670

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3.2k

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scRNA-seq SEURAT

updated 5.9 years ago by Steve Lianoglou ★ 13k • written 5.9 years ago by Bogdan ▴ 670

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1.5k

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rnaseq scRNA-seq

updated 6.4 years ago by Aaron Lun ★ 28k • written 6.4 years ago by Bogdan ▴ 670

30 results • Page 1 of 1

Recent ...

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Comment: Identical samples after deseq2 batch effect removal by Michael Love 42k

I'm adding my comment to the threaded section ... I don't have any suggestions here but whatever method you're using is not appropriate up…

Comment: ANOVA like approach of edgeR by Yunshun Chen ▴ 880

If you do it this way, the dispersion estimates would be much higher than they should (as the cell type difference is not accounted for in …

Comment: ANOVA like approach of edgeR by SamGG ▴ 350

Simply remove the cell type from the model. design <- model.matrix(~targets$Status)

Answer: ANOVA like approach of edgeR by Yunshun Chen ▴ 880

You could try the followings: > design <- model.matrix(~ 0 + group) > contrast <- makeContrasts(PvsL = 0.5*(L.pregnant + B.pregnan…

Answer: Identical samples after deseq2 batch effect removal by maripane • 0

Thanks Michael, so is there a way to work around this issue? Can I somehow make sure I can remove this batch effects without overcorrecti…

Votes

Answer: ANOVA like approach of edgeR

A: ANOVA-like test with edgeR

Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data

A: TopGO: How to retrieve the gene list related to a GO ID ?

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