Showing : scRNA-Seq • reset
4
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5
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2.3k
views
emptyDrops identified less non-empty cells with lower total UMI counts?
DropletUtils scRNA-seq emptyDrops simplesinglecell cell calling
updated 4.1 years ago by ★ 28k • written 5.2 years ago by ▴ 140
5
votes
3
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1.6k
views
Latent factors for differential expression
deseq2 zinbwave 10X scRNA-seq Differential expression
updated 4.4 years ago by 42k • written 4.4 years ago by ▴ 20
0
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2
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3.5k
views
cmdscale() error: NA values not allowed in 'd', ask for help.
cmdscale zinbwave scRNA-seq single cell sequencing RNA-seq
updated 4.4 years ago by ▴ 980 • written 4.4 years ago by ▴ 10
0
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0
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818
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clustering of scRNAseq gene expression at multiple time points
scRNA-seq time series
4.4 years ago Bogdan ▴ 670
2
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4
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1.1k
views
scRNA-seq question, assayData() error
assayData() scRNA-seq single cell sequencing assayData Bioconductor
updated 4.5 years ago by ★ 4.0k • written 4.5 years ago by ▴ 10
3
votes
6
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3.4k
views
Carry over variable features when converting FastMNN SCE object to Seurat object
mnn batchelor scrna-seq seurat
updated 4.5 years ago by ★ 28k • written 4.5 years ago by • 0
7
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3
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6.4k
views
Downsample or not to downsample?
scrna-seq downsampleBatches scran
updated 4.6 years ago by ★ 28k • written 4.6 years ago by ▴ 40
3
votes
11
replies
2.2k
views
normalization methods for scRNA-seq and RNA-seq in specific cases of increased global transcription
RNA-seq scRNA-seq
updated 4.8 years ago by ★ 28k • written 4.8 years ago by ▴ 670
3
votes
3
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1.8k
views
fastMNN based correction for large multi-run experiment requires a similar population set in all the individual datasets?
scrna-seq integration batch correction
updated 4.8 years ago by ★ 28k • written 4.9 years ago by ▴ 40
2
votes
2
replies
2.0k
views
Subclustering after MNN batch-correction
batchelor mnn scrna-seq
updated 2.3 years ago by ▴ 40 • written 4.9 years ago by • 0
4
votes
2
replies
890
views
scRNA-seq analysis : the IDENTITY of the CLUSTERS across MULTIPLE EXPERIMENTS
scRNA-seq
updated 4.9 years ago by ★ 28k • written 4.9 years ago by ▴ 670
1
vote
3
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1.6k
views
comparing 2 models with confounders with MAST (scRNA-seq DEA)
scRNA-seq MAST confounders
updated 4.9 years ago by ▴ 270 • written 4.9 years ago by ▴ 10
0
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0
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1.1k
views
Job: Bioinformatics Scientist, CNS Transcriptomics at Alnylam Pharmaceuticals, Cambridge MA, USA
scRNA-seq CNS transcriptomics RNAi Job
4.9 years ago Joseph Barry ▴ 10
2
votes
1
reply
2.3k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq scater scran rna-seq MNN
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 60
2
votes
2
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3.0k
views
DE analysis for 10X scRNA-seq data with multiple conditions and multiple replicates
scRNA-seq Seurat DE
updated 5.2 years ago by ★ 28k • written 5.2 years ago by • 0
0
votes
1
reply
1.0k
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emptyDrops result is full NAs
scran dropletUtils scater scRNA-Seq
5.5 years ago hamza_karakurt ▴ 60
3
votes
3
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2.5k
views
edgeR: Strange volcano plot
edger scRNA-seq DGEA
updated 5.6 years ago by ★ 28k • written 5.6 years ago by • 0
4
votes
2
replies
2.9k
views
When to combine samples in the pre-processing of 10x scRNA-seq data?
10x scrna-seq
updated 5.6 years ago by ★ 28k • written 5.6 years ago by ▴ 70
8
votes
4
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3.0k
views
Usage of doubletCells() function before or after the batch correction?
scater scran scRNA-Seq doubletCells
updated 5.6 years ago by ★ 28k • written 5.6 years ago by ▴ 60
4
votes
5
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2.1k
views
Using SC3 with batch corrected MNN values
SC3 Scater Scran scRNA-Seq Batch Correction
updated 5.6 years ago by ▴ 150 • written 5.6 years ago by ▴ 60
1
vote
2
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1.7k
views
Dunn Index for Clusters from scRNA-Seq
scRNA-Seq clustering scater scran dunn index
updated 5.7 years ago by ★ 28k • written 5.7 years ago by ▴ 60
5
votes
5
replies
6.9k
views
Differential Expression Analysis between conditions of single cell RNA-Seq
deseq2 scRNA-Seq RNA-Seq differential expression analysis
updated 5.7 years ago by 42k • written 5.7 years ago by ▴ 60
2
votes
5
replies
1.8k
views
Modularity values of clusters and Differential Expression in scRNA-Seq
scater scran igraph scRNA-Seq rots
updated 5.7 years ago by ★ 28k • written 5.7 years ago by ▴ 60
3
votes
3
replies
2.0k
views
Enrichment Analysis with only GeneSymbols
R GSEA rna-seq scRna-Seq
updated 5.7 years ago by ★ 3.0k • written 5.7 years ago by ▴ 60
2
votes
5
replies
4.5k
views
Adding labels on clusters in a t-SNE plot and changing colors
scran scater Rtsne ggplot2 scRNA-Seq
updated 2.2 years ago by ▴ 60 • written 5.8 years ago by ▴ 60
2
votes
4
replies
2.7k
views
Silhouette Plots for Clustering Quality (Multiple Algorithm)
scRNA-Seq RNA-Seq Clustering Silhouette Plot
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 60
0
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3
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1.7k
views
about scRNA-seq, SEURAT and CCA
scRNA-seq
updated 5.9 years ago by 67k • written 5.9 years ago by ▴ 670
1
vote
1
reply
1.5k
views
gene counts in Seurat after RunCCA() and AlignSubspace()
scRNA-seq seurat CCA
updated 5.9 years ago by ★ 28k • written 5.9 years ago by ▴ 670
0
votes
4
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3.2k
views
scRNA-seq: a question about the names of the columns in a Seurat object
scRNA-seq SEURAT
updated 5.9 years ago by ★ 13k • written 5.9 years ago by ▴ 670
0
votes
3
replies
1.5k
views
single cell RNA-seq pipeline
rnaseq scRNA-seq
updated 6.4 years ago by ★ 28k • written 6.4 years ago by ▴ 670
30 results • Page 1 of 1
Recent ...
Replies
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
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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