Showing : scrna-seq • reset
4
votes
5
replies
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
replies
1.6k
views
Latent factors for differential expression
deseq2 zinbwave 10X scRNA-seq Differential expression
updated 4.4 years ago by 43k • written 4.4 years ago by ▴ 20
0
votes
2
replies
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 4.5 years ago by ▴ 10
0
votes
0
replies
821
views
clustering of scRNAseq gene expression at multiple time points
scRNA-seq time series
4.4 years ago Bogdan ▴ 670
2
votes
4
replies
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
replies
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
votes
3
replies
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
replies
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
891
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
replies
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
votes
0
replies
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
replies
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
views
emptyDrops result is full NAs
scran dropletUtils scater scRNA-Seq
5.5 years ago hamza_karakurt ▴ 60
3
votes
3
replies
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
replies
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
replies
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
replies
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 43k • 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 5.8 years ago by ★ 3.0k • written 5.8 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 2.3 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
votes
3
replies
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
replies
3.2k
views
scRNA-seq: a question about the names of the columns in a Seurat object
scRNA-seq SEURAT
updated 6.0 years ago by ★ 13k • written 6.0 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
Answer: Deseq2 res Function by Michael Love 43k
> Does this mean the young and KO groups were numerators and denominators in the analysis, respectively? Read over the vignette and work…
Answer: ANOVA like approach of edgeR by Gordon Smyth 51k
You need to clarify whether interactions are present for the two factors in your study. In the two factors do not interact, then the code y…
Answer: Create Illmina bead summary data by Gordon Smyth 51k
GenomeStudio produces IDAT files that you can read using the `read.idat` function in limma. That is the recommended way to read GenomeStudi…
Comment: Help with RSEM counts: do I transpose matrix? by NB • 0
OK thank you.
Comment: Help with RSEM counts: do I transpose matrix? by James W. MacDonald 67k
You can ask here, but please read the `DESeq2` vignette first, which should answer most questions.
Votes
Answer: Deseq2 res Function
Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification
Answer: ANOVA like approach of edgeR
Answer: ANOVA like approach of edgeR
Comment: ANOVA like approach of edgeR
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