Showing : scRNA-seq • reset
4
votes
5
replies
893
views
emptyDrops identified less non-empty cells with lower total UMI counts?
DropletUtils scRNA-seq emptyDrops simplesinglecell cell calling
updated 19 months ago by ★ 27k • written 2.7 years ago by ▴ 140
3
votes
3
replies
438
views
Latent factors for differential expression
deseq2 zinbwave 10X scRNA-seq Differential expression
updated 22 months ago by 36k • written 22 months ago by ▴ 20
0
votes
2
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1.5k
views
cmdscale() error: NA values not allowed in 'd', ask for help.
cmdscale zinbwave scRNA-seq single cell sequencing RNA-seq
updated 22 months ago by ▴ 890 • written 23 months ago by ▴ 10
0
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0
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245
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clustering of scRNAseq gene expression at multiple time points
scRNA-seq time series
22 months ago Bogdan ▴ 640
2
votes
4
replies
361
views
scRNA-seq question, assayData() error
assayData() scRNA-seq single cell sequencing assayData Bioconductor
updated 23 months ago by 3.5k • written 23 months ago by ▴ 10
3
votes
6
replies
1.0k
views
Carry over variable features when converting FastMNN SCE object to Seurat object
mnn batchelor scrna-seq seurat
updated 24 months ago by ★ 27k • written 24 months ago by • 0
4
votes
3
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1.1k
views
Downsample or not to downsample?
scrna-seq downsampleBatches scran
updated 2.0 years ago by ★ 27k • written 2.0 years ago by ▴ 20
3
votes
11
replies
668
views
normalization methods for scRNA-seq and RNA-seq in specific cases of increased global transcription
RNA-seq scRNA-seq
updated 2.3 years ago by ★ 27k • written 2.3 years ago by ▴ 640
2
votes
3
replies
398
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 2.3 years ago by ★ 27k • written 2.3 years ago by ▴ 20
0
votes
1
reply
444
views
Subclustering after MNN batch-correction
batchelor mnn scrna-seq
updated 2.3 years ago by ★ 27k • written 2.3 years ago by • 0
4
votes
2
replies
302
views
scRNA-seq analysis : the IDENTITY of the CLUSTERS across MULTIPLE EXPERIMENTS
scRNA-seq
updated 2.4 years ago by ★ 27k • written 2.4 years ago by ▴ 640
1
vote
3
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500
views
comparing 2 models with confounders with MAST (scRNA-seq DEA)
scRNA-seq MAST confounders
updated 2.4 years ago by ▴ 260 • written 2.4 years ago by ▴ 10
0
votes
0
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318
views
Job: Bioinformatics Scientist, CNS Transcriptomics at Alnylam Pharmaceuticals, Cambridge MA, USA
scRNA-seq CNS transcriptomics RNAi Job
2.4 years ago Joseph Barry ▴ 10
2
votes
1
reply
816
views
Batch Corrections (MNN) with TPM values
scRNA-Seq scater scran rna-seq MNN
updated 2.6 years ago by ★ 27k • written 2.6 years ago by ▴ 50
2
votes
2
replies
1.6k
views
DE analysis for 10X scRNA-seq data with multiple conditions and multiple replicates
scRNA-seq Seurat DE
updated 2.7 years ago by ★ 27k • written 2.7 years ago by • 0
0
votes
1
reply
340
views
emptyDrops result is full NAs
scran dropletUtils scater scRNA-Seq
2.9 years ago hamza_karakurt ▴ 50
3
votes
3
replies
1.3k
views
edgeR: Strange volcano plot
edger scRNA-seq DGEA
updated 3.0 years ago by ★ 27k • written 3.0 years ago by • 0
4
votes
2
replies
778
views
When to combine samples in the pre-processing of 10x scRNA-seq data?
10x scrna-seq
updated 3.0 years ago by ★ 27k • written 3.1 years ago by ▴ 60
4
votes
4
replies
837
views
Usage of doubletCells() function before or after the batch correction?
scater scran scRNA-Seq doubletCells
updated 3.1 years ago by ★ 27k • written 3.1 years ago by ▴ 50
4
votes
5
replies
845
views
Using SC3 with batch corrected MNN values
SC3 Scater Scran scRNA-Seq Batch Correction
updated 3.1 years ago by ▴ 150 • written 3.1 years ago by ▴ 50
1
vote
2
replies
703
views
Dunn Index for Clusters from scRNA-Seq
scRNA-Seq clustering scater scran dunn index
updated 3.2 years ago by ★ 27k • written 3.2 years ago by ▴ 50
5
votes
5
replies
2.7k
views
Differential Expression Analysis between conditions of single cell RNA-Seq
deseq2 scRNA-Seq RNA-Seq differential expression analysis
updated 3.2 years ago by 36k • written 3.2 years ago by ▴ 50
2
votes
5
replies
667
views
Modularity values of clusters and Differential Expression in scRNA-Seq
scater scran igraph scRNA-Seq rots
updated 3.2 years ago by ★ 27k • written 3.2 years ago by ▴ 50
3
votes
3
replies
653
views
Enrichment Analysis with only GeneSymbols
R GSEA rna-seq scRna-Seq
updated 3.2 years ago by ★ 2.6k • written 3.2 years ago by ▴ 50
1
vote
2
replies
1.7k
views
Adding labels on clusters in a t-SNE plot and changing colors
scran scater Rtsne ggplot2 scRNA-Seq
updated 3.2 years ago by ★ 27k • written 3.2 years ago by ▴ 50
2
votes
4
replies
1.2k
views
Silhouette Plots for Clustering Quality (Multiple Algorithm)
scRNA-Seq RNA-Seq Clustering Silhouette Plot
updated 3.3 years ago by ★ 27k • written 3.3 years ago by ▴ 50
0
votes
3
replies
789
views
about scRNA-seq, SEURAT and CCA
scRNA-seq
updated 3.3 years ago by 59k • written 3.3 years ago by ▴ 640
1
vote
1
reply
701
views
gene counts in Seurat after RunCCA() and AlignSubspace()
scRNA-seq seurat CCA
updated 3.4 years ago by ★ 27k • written 3.4 years ago by ▴ 640
0
votes
4
replies
1.4k
views
scRNA-seq: a question about the names of the columns in a Seurat object
scRNA-seq SEURAT
updated 3.4 years ago by 13k • written 3.4 years ago by ▴ 640
0
votes
3
replies
537
views
single cell RNA-seq pipeline
rnaseq scRNA-seq
updated 3.8 years ago by ★ 27k • written 3.8 years ago by ▴ 640
30 results • Page 1 of 1
Recent ...
Replies
Answer: how to understand cpm=1 and how filterByExpr works? by gowthamee • 0
I found the following two articles very helpful in explaining the functions "cpm" and "filterByExpr" Article#1: From reads to genes to pat…
Comment: different results in DESeq2 when comparing groups in two ways by zohreh.fazelan • 0
Thank you for your response. But I have few comparisons in which there are more significantly expressed genes in the socond way compared to…
Comment: lmFit, continuous exposure, adjustment covariates by Gordon Smyth 45k
Your code `t(dat[43:ncol(dat)]` is not even syntactically correct. It could not possibly run in R. You need to create an expression matrix…
Comment: Handling of missing values in limma by Gordon Smyth 45k
limma uses all the observations. There's nothing complicated about it. limma does not remove any persons from the analysis. I did not tel…
Answer: after calcNormFactors with EdgeR, how to get TMM normalized matrix? by Gordon Smyth 45k
There's no such thing as a "TMM normalized matrix" or "normalized values" in edgeR. Have you read the edgeR User's Guide for how analyses a…
Votes
Answer: Using featureCounts and downloading Rsubread
Answer: different results in DESeq2 when comparing groups in two ways
Comment: edgeR: the F-statistics changed after removing lowly expressed gene
Answer: Get MANE transcripts from TxDb.Hsapiens.UCSC.hg38.knownGene
Answer: Get MANE transcripts from TxDb.Hsapiens.UCSC.hg38.knownGene
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