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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
Aaron Lun
★ 27k • written 2.7 years ago by
C T
▴ 140
3
votes
3
replies
438
views
Latent factors for differential expression
deseq2
zinbwave
10X
scRNA-seq
Differential expression
updated 22 months ago by
Michael Love
36k • written 22 months ago by
vincent.croset
▴ 20
0
votes
2
replies
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
davide risso
▴ 890 • written 23 months ago by
Wagaa
▴ 10
0
votes
0
replies
245
views
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
Kevin Blighe
3.5k • written 23 months ago by
Wagaa
▴ 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
Aaron Lun
★ 27k • written 24 months ago by
heir_of_isildur88
• 0
4
votes
3
replies
1.1k
views
Downsample or not to downsample?
scrna-seq
downsampleBatches
scran
updated 2.0 years ago by
Aaron Lun
★ 27k • written 2.0 years ago by
p.joshi
▴ 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
Aaron Lun
★ 27k • written 2.3 years ago by
Bogdan
▴ 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
Aaron Lun
★ 27k • written 2.3 years ago by
p.joshi
▴ 20
0
votes
1
reply
444
views
Subclustering after MNN batch-correction
batchelor
mnn
scrna-seq
updated 2.3 years ago by
Aaron Lun
★ 27k • written 2.3 years ago by
heir_of_isildur88
• 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
Aaron Lun
★ 27k • written 2.4 years ago by
Bogdan
▴ 640
1
vote
3
replies
500
views
comparing 2 models with confounders with MAST (scRNA-seq DEA)
scRNA-seq
MAST
confounders
updated 2.4 years ago by
Andrew_McDavid
▴ 260 • written 2.4 years ago by
ramonmassoni
▴ 10
0
votes
0
replies
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
Aaron Lun
★ 27k • written 2.6 years ago by
hamza_karakurt
▴ 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
Aaron Lun
★ 27k • written 2.7 years ago by
ilee8
• 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
Aaron Lun
★ 27k • written 3.0 years ago by
cronanz
• 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
Aaron Lun
★ 27k • written 3.1 years ago by
jma1991
▴ 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
Aaron Lun
★ 27k • written 3.1 years ago by
hamza_karakurt
▴ 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
Vladimir Kiselev
▴ 150 • written 3.1 years ago by
hamza_karakurt
▴ 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
Aaron Lun
★ 27k • written 3.2 years ago by
hamza_karakurt
▴ 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
Michael Love
36k • written 3.2 years ago by
hamza_karakurt
▴ 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
Aaron Lun
★ 27k • written 3.2 years ago by
hamza_karakurt
▴ 50
3
votes
3
replies
653
views
Enrichment Analysis with only GeneSymbols
R
GSEA
rna-seq
scRna-Seq
updated 3.2 years ago by
Peter Langfelder
★ 2.6k • written 3.2 years ago by
hamza_karakurt
▴ 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
Aaron Lun
★ 27k • written 3.2 years ago by
hamza_karakurt
▴ 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
Aaron Lun
★ 27k • written 3.3 years ago by
hamza_karakurt
▴ 50
0
votes
3
replies
789
views
about scRNA-seq, SEURAT and CCA
scRNA-seq
updated 3.3 years ago by
James W. MacDonald
59k • written 3.3 years ago by
Bogdan
▴ 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
Aaron Lun
★ 27k • written 3.4 years ago by
Bogdan
▴ 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
Steve Lianoglou
13k • written 3.4 years ago by
Bogdan
▴ 640
0
votes
3
replies
537
views
single cell RNA-seq pipeline
rnaseq
scRNA-seq
updated 3.8 years ago by
Aaron Lun
★ 27k • written 3.8 years ago by
Bogdan
▴ 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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