Showing : scRNA-seq • reset
4
votes
5
replies
531
views
emptyDrops identified less non-empty cells with lower total UMI counts?
DropletUtils scRNA-seq emptyDrops simplesinglecell cell calling
updated 8 months ago by ★ 26k • written 22 months ago by ▴ 140
3
votes
3
replies
231
views
Latent factors for differential expression
deseq2 zinbwave 10X scRNA-seq Differential expression
updated 11 months ago by 33k • written 11 months ago by ▴ 20
0
votes
2
replies
453
views
cmdscale() error: NA values not allowed in 'd', ask for help.
cmdscale zinbwave scRNA-seq single cell sequencing RNA-seq
updated 11 months ago by ▴ 870 • written 12 months ago by ▴ 10
0
votes
0
replies
106
views
clustering of scRNAseq gene expression at multiple time points
scRNA-seq time series
11 months ago Bogdan ▴ 610
2
votes
4
replies
195
views
scRNA-seq question, assayData() error
assayData() scRNA-seq single cell sequencing assayData Bioconductor
updated 12 months ago by 3.1k • written 12 months ago by ▴ 10
3
votes
6
replies
416
views
Carry over variable features when converting FastMNN SCE object to Seurat object
mnn batchelor scrna-seq seurat
updated 13 months ago by ★ 26k • written 13 months ago by • 0
4
votes
3
replies
212
views
Downsample or not to downsample?
scrna-seq downsampleBatches scran
updated 13 months ago by ★ 26k • written 13 months ago by ▴ 20
3
votes
11
replies
382
views
normalization methods for scRNA-seq and RNA-seq in specific cases of increased global transcription
RNA-seq scRNA-seq
updated 17 months ago by ★ 26k • written 17 months ago by ▴ 610
2
votes
3
replies
170
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 17 months ago by ★ 26k • written 17 months ago by ▴ 20
0
votes
1
reply
183
views
Subclustering after MNN batch-correction
batchelor mnn scrna-seq
updated 17 months ago by ★ 26k • written 17 months ago by • 0
4
votes
2
replies
184
views
scRNA-seq analysis : the IDENTITY of the CLUSTERS across MULTIPLE EXPERIMENTS
scRNA-seq
updated 17 months ago by ★ 26k • written 17 months ago by ▴ 610
1
vote
3
replies
272
views
comparing 2 models with confounders with MAST (scRNA-seq DEA)
scRNA-seq MAST confounders
updated 17 months ago by ▴ 260 • written 17 months ago by ▴ 10
0
votes
0
replies
164
views
Job: Bioinformatics Scientist, CNS Transcriptomics at Alnylam Pharmaceuticals, Cambridge MA, USA
scRNA-seq CNS transcriptomics RNAi Job
17 months ago Joseph Barry ▴ 10
2
votes
1
reply
366
views
Batch Corrections (MNN) with TPM values
scRNA-Seq scater scran rna-seq MNN
updated 20 months ago by ★ 26k • written 20 months ago by ▴ 50
2
votes
2
replies
827
views
DE analysis for 10X scRNA-seq data with multiple conditions and multiple replicates
scRNA-seq Seurat DE
updated 21 months ago by ★ 26k • written 21 months ago by • 0
0
votes
1
reply
213
views
emptyDrops result is full NAs
scran dropletUtils scater scRNA-Seq
2.0 years ago hamza_karakurt ▴ 50
3
votes
3
replies
860
views
edgeR: Strange volcano plot
edger scRNA-seq DGEA
updated 2.1 years ago by ★ 26k • written 2.1 years ago by • 0
4
votes
2
replies
443
views
When to combine samples in the pre-processing of 10x scRNA-seq data?
10x scrna-seq
updated 2.2 years ago by ★ 26k • written 2.2 years ago by ▴ 60
4
votes
4
replies
485
views
Usage of doubletCells() function before or after the batch correction?
scater scran scRNA-Seq doubletCells
updated 2.2 years ago by ★ 26k • written 2.2 years ago by ▴ 50
4
votes
5
replies
561
views
Using SC3 with batch corrected MNN values
SC3 Scater Scran scRNA-Seq Batch Correction
updated 2.2 years ago by ▴ 150 • written 2.2 years ago by ▴ 50
1
vote
2
replies
477
views
Dunn Index for Clusters from scRNA-Seq
scRNA-Seq clustering scater scran dunn index
updated 2.3 years ago by ★ 26k • written 2.3 years ago by ▴ 50
5
votes
5
replies
1.6k
views
Differential Expression Analysis between conditions of single cell RNA-Seq
deseq2 scRNA-Seq RNA-Seq differential expression analysis
updated 2.3 years ago by 33k • written 2.3 years ago by ▴ 50
2
votes
5
replies
404
views
Modularity values of clusters and Differential Expression in scRNA-Seq
scater scran igraph scRNA-Seq rots
updated 2.3 years ago by ★ 26k • written 2.3 years ago by ▴ 50
3
votes
3
replies
440
views
Enrichment Analysis with only GeneSymbols
R GSEA rna-seq scRna-Seq
updated 2.3 years ago by ★ 2.6k • written 2.3 years ago by ▴ 50
1
vote
2
replies
1.1k
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 ★ 26k • written 2.3 years ago by ▴ 50
2
votes
4
replies
872
views
Silhouette Plots for Clustering Quality (Multiple Algorithm)
scRNA-Seq RNA-Seq Clustering Silhouette Plot
updated 2.4 years ago by ★ 26k • written 2.4 years ago by ▴ 50
0
votes
3
replies
499
views
about scRNA-seq, SEURAT and CCA
scRNA-seq
updated 2.4 years ago by 57k • written 2.4 years ago by ▴ 610
1
vote
1
reply
314
views
gene counts in Seurat after RunCCA() and AlignSubspace()
scRNA-seq seurat CCA
updated 2.5 years ago by ★ 26k • written 2.5 years ago by ▴ 610
0
votes
4
replies
784
views
scRNA-seq: a question about the names of the columns in a Seurat object
scRNA-seq SEURAT
updated 2.5 years ago by 13k • written 2.5 years ago by ▴ 610
0
votes
3
replies
349
views
single cell RNA-seq pipeline
rnaseq scRNA-seq
updated 2.9 years ago by ★ 26k • written 2.9 years ago by ▴ 610
30 results • Page 1 of 1
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Comment: pathview: unable to use option "out.suffix" by 文祥 • 0
Add coment about sessionInfo R version 4.1.0 (2021-05-18) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 10.16 …
Comment: To retrieve the transcript from gff file with the longest isoform by Aneesha • 0
Okay, Thank You
Comment: how to plot multiple RLEs on same plot? by xiaofeiwang18266 ▴ 20
Thanks a lot!
Answer: Data input for aracne2regulon function in viper package by reef103 • 0
Hi @luna_p , I'm sorry I didn;t see this before. The error might be due to a lack of match between the genes in the network (regulators and…
Comment: deseq2 normalized data with heatmap by Kevin Blighe 3.1k
Hey Ian, specifically just for the heatmap and/or the clustering, we can additionally scale and center the `vsd` or `rld` data. The `scale…
Votes
Answer: Difference in mixed test for fry vs mroast
A: DESeq2 variance transformation error and plot dispersion Estimate
Error in DESeqDataSet : some values in assay are not integers
A: Error in DESeqDataSet : some values in assay are not integers
A: Error in DESeqDataSet : some values in assay are not integers
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