Bioconductor ScRNA-seq

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DropletUtils scRNA-seq emptyDrops simplesinglecell cell calling

updated 4.0 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 4.3 years ago by Michael Love 42k • written 4.3 years ago by vincent.croset ▴ 20

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cmdscale zinbwave scRNA-seq single cell sequencing RNA-seq

updated 4.3 years ago by davide risso ▴ 980 • written 4.4 years ago by Wagaa ▴ 10

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810

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scRNA-seq time series

4.3 years ago Bogdan ▴ 670

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1.1k

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assayData() scRNA-seq single cell sequencing assayData Bioconductor

updated 4.4 years ago by Kevin Blighe ★ 4.0k • written 4.4 years ago by Wagaa ▴ 10

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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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scrna-seq downsampleBatches scran

updated 4.5 years ago by Aaron Lun ★ 28k • written 4.5 years ago by p.joshi ▴ 40

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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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scrna-seq integration batch correction

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

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1.9k

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batchelor mnn scrna-seq

updated 2.3 years ago by Guandong Shang ▴ 40 • written 4.8 years ago by heir_of_isildur88 • 0

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880

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scRNA-seq

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

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scRNA-seq MAST confounders

updated 4.8 years ago by Andrew_McDavid ▴ 270 • written 4.8 years ago by ramonmassoni ▴ 10

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scRNA-seq CNS transcriptomics RNAi Job

4.8 years ago Joseph Barry ▴ 10

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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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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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994

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scran dropletUtils scater scRNA-Seq

5.4 years ago hamza_karakurt ▴ 60

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edger scRNA-seq DGEA

updated 5.5 years ago by Aaron Lun ★ 28k • written 5.5 years ago by cronanz • 0

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2.9k

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10x scrna-seq

updated 5.5 years ago by Aaron Lun ★ 28k • written 5.5 years ago by jma1991 ▴ 70

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2.9k

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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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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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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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1.9k

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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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scran scater Rtsne ggplot2 scRNA-Seq

updated 2.2 years ago by jamie.gearing ▴ 60 • written 5.7 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 5.8 years ago by James W. MacDonald 67k • written 5.8 years ago by Bogdan ▴ 670

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1.4k

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scRNA-seq seurat CCA

updated 5.8 years ago by Aaron Lun ★ 28k • written 5.8 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 6.3 years ago by Aaron Lun ★ 28k • written 6.3 years ago by Bogdan ▴ 670

30 results • Page 1 of 1

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Comment: Combining RNAseq and microarray data using edgeR/limma-voom by Adam Marstrand • 0

Thank you!

Comment: Combining RNAseq and microarray data using edgeR/limma-voom by Adam Marstrand • 0

Hi Gordon, Thanks for the answer! This makes a lot of sense. Your suggested pipeline (separate processing of datasets -> gene set analyses…

Comment: How many of my genes from my gene list are in each KEGG pathway? by josephasmith1310 • 0

> You can compare the number in the column setSize versus the number of > genes in core_enrichment. The former corresponds to the number of…

Comment: EuroBioC2024 abstract submission is open! by Esperan • 0

Great information about the EuroBioC2024 conference! https://openreview.net/group?id=bioconductor.org/EuroBioC/2024/Conferences [slope](htt…

Answer: Combining RNAseq and microarray data using edgeR/limma-voom by Gordon Smyth 51k

I agree with James, although I tend to combine analyses using geneset tests rather than by meta analysis tools like GeneMeta. > My questio…

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Answer: Combining RNAseq and microarray data using edgeR/limma-voom

Answer: How do I merge a list of GRanges?

A: p.adjust BH generates duplicate values

Answer: Adjusted p-values become NA when sub-setting samples

Comment: Suggestion for FGSEA and GSEA creation for C57BL/6J Mice

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