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scRNA-Seq
•
reset
3
votes
11
replies
1.8k
views
normalization methods for scRNA-seq and RNA-seq in specific cases of increased global transcription
RNA-seq
scRNA-seq
updated 4.2 years ago by
Aaron Lun
★ 28k • written 4.2 years ago by
Bogdan
▴ 670
3
votes
6
replies
2.9k
views
Carry over variable features when converting FastMNN SCE object to Seurat object
mnn
batchelor
scrna-seq
seurat
updated 3.9 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
heir_of_isildur88
• 0
4
votes
5
replies
1.7k
views
Using SC3 with batch corrected MNN values
SC3
Scater
Scran
scRNA-Seq
Batch Correction
updated 5.0 years ago by
Vladimir Kiselev
▴ 150 • written 5.0 years ago by
hamza_karakurt
▴ 50
4
votes
5
replies
1.9k
views
emptyDrops identified less non-empty cells with lower total UMI counts?
DropletUtils
scRNA-seq
emptyDrops
simplesinglecell
cell calling
updated 3.5 years ago by
Aaron Lun
★ 28k • written 4.6 years ago by
C T
▴ 140
2
votes
5
replies
3.7k
views
Adding labels on clusters in a t-SNE plot and changing colors
scran
scater
Rtsne
ggplot2
scRNA-Seq
updated 20 months ago by
jamie.gearing
▴ 60 • written 5.2 years ago by
hamza_karakurt
▴ 50
2
votes
5
replies
1.4k
views
Modularity values of clusters and Differential Expression in scRNA-Seq
scater
scran
igraph
scRNA-Seq
rots
updated 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
hamza_karakurt
▴ 50
5
votes
5
replies
5.7k
views
Differential Expression Analysis between conditions of single cell RNA-Seq
deseq2
scRNA-Seq
RNA-Seq
differential expression analysis
updated 5.1 years ago by
Michael Love
41k • written 5.1 years ago by
hamza_karakurt
▴ 50
0
votes
4
replies
2.9k
views
scRNA-seq: a question about the names of the columns in a Seurat object
scRNA-seq
SEURAT
updated 5.4 years ago by
Steve Lianoglou
★ 13k • written 5.4 years ago by
Bogdan
▴ 670
2
votes
4
replies
2.3k
views
Silhouette Plots for Clustering Quality (Multiple Algorithm)
scRNA-Seq
RNA-Seq
Clustering
Silhouette Plot
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
hamza_karakurt
▴ 50
8
votes
4
replies
2.2k
views
Usage of doubletCells() function before or after the batch correction?
scater
scran
scRNA-Seq
doubletCells
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
hamza_karakurt
▴ 50
2
votes
4
replies
932
views
scRNA-seq question, assayData() error
assayData()
scRNA-seq
single cell sequencing
assayData
Bioconductor
updated 3.9 years ago by
Kevin Blighe
★ 3.9k • written 3.9 years ago by
Wagaa
▴ 10
5
votes
3
replies
1.3k
views
Latent factors for differential expression
deseq2
zinbwave
10X
scRNA-seq
Differential expression
updated 3.8 years ago by
Michael Love
41k • written 3.8 years ago by
vincent.croset
▴ 20
0
votes
3
replies
1.5k
views
about scRNA-seq, SEURAT and CCA
scRNA-seq
updated 5.3 years ago by
James W. MacDonald
65k • written 5.3 years ago by
Bogdan
▴ 670
3
votes
3
replies
1.5k
views
Enrichment Analysis with only GeneSymbols
R
GSEA
rna-seq
scRna-Seq
updated 5.1 years ago by
Peter Langfelder
★ 3.0k • written 5.1 years ago by
hamza_karakurt
▴ 50
3
votes
3
replies
2.2k
views
edgeR: Strange volcano plot
edger
scRNA-seq
DGEA
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
cronanz
• 0
1
vote
3
replies
1.2k
views
comparing 2 models with confounders with MAST (scRNA-seq DEA)
scRNA-seq
MAST
confounders
updated 4.3 years ago by
Andrew_McDavid
▴ 270 • written 4.3 years ago by
ramonmassoni
▴ 10
3
votes
3
replies
1.5k
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 4.2 years ago by
Aaron Lun
★ 28k • written 4.3 years ago by
p.joshi
▴ 40
7
votes
3
replies
4.7k
views
Downsample or not to downsample?
scrna-seq
downsampleBatches
scran
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.0 years ago by
p.joshi
▴ 40
0
votes
3
replies
1.3k
views
single cell RNA-seq pipeline
rnaseq
scRNA-seq
updated 5.8 years ago by
Aaron Lun
★ 28k • written 5.8 years ago by
Bogdan
▴ 670
2
votes
2
replies
2.7k
views
DE analysis for 10X scRNA-seq data with multiple conditions and multiple replicates
scRNA-seq
Seurat
DE
updated 4.6 years ago by
Aaron Lun
★ 28k • written 4.6 years ago by
ilee8
• 0
4
votes
2
replies
2.3k
views
When to combine samples in the pre-processing of 10x scRNA-seq data?
10x
scrna-seq
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
jma1991
▴ 70
4
votes
2
replies
726
views
scRNA-seq analysis : the IDENTITY of the CLUSTERS across MULTIPLE EXPERIMENTS
scRNA-seq
updated 4.3 years ago by
Aaron Lun
★ 28k • written 4.3 years ago by
Bogdan
▴ 670
1
vote
2
replies
1.4k
views
Dunn Index for Clusters from scRNA-Seq
scRNA-Seq
clustering
scater
scran
dunn index
updated 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
hamza_karakurt
▴ 50
2
votes
2
replies
1.5k
views
Subclustering after MNN batch-correction
batchelor
mnn
scrna-seq
updated 20 months ago by
Guandong Shang
▴ 40 • written 4.3 years ago by
heir_of_isildur88
• 0
0
votes
2
replies
3.1k
views
cmdscale() error: NA values not allowed in 'd', ask for help.
cmdscale
zinbwave
scRNA-seq
single cell sequencing
RNA-seq
updated 3.8 years ago by
davide risso
▴ 950 • written 3.9 years ago by
Wagaa
▴ 10
1
vote
1
reply
1.3k
views
gene counts in Seurat after RunCCA() and AlignSubspace()
scRNA-seq
seurat
CCA
updated 5.3 years ago by
Aaron Lun
★ 28k • written 5.3 years ago by
Bogdan
▴ 670
2
votes
1
reply
1.9k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq
scater
scran
rna-seq
MNN
updated 4.5 years ago by
Aaron Lun
★ 28k • written 4.5 years ago by
hamza_karakurt
▴ 50
0
votes
1
reply
820
views
emptyDrops result is full NAs
scran
dropletUtils
scater
scRNA-Seq
4.9 years ago
hamza_karakurt
▴ 50
0
votes
0
replies
852
views
Job:
Bioinformatics Scientist, CNS Transcriptomics at Alnylam Pharmaceuticals, Cambridge MA, USA
scRNA-seq
CNS
transcriptomics
RNAi
Job
4.3 years ago
Joseph Barry
▴ 10
0
votes
0
replies
652
views
clustering of scRNAseq gene expression at multiple time points
scRNA-seq
time series
3.8 years ago
Bogdan
▴ 670
30 results • Page
1 of 1
Recent ...
Replies
Comment: Which input file is used for DGEList in EgdeR?
by
i.atanasoai
• 0
Understood, Thank you very much for the reply, very kind.
Comment: Which input file is used for DGEList in EgdeR?
by
Michael Love
41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Michael Love
41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts
by
Michael Love
41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
If the counts are too low it in one group then you can't make the comparison either way (whether they are filtered out or just under-powere…
Votes
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
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