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scRNA-Seq
•
reset
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 3.4 years ago by
Aaron Lun
★ 28k • written 4.6 years ago by
C T
▴ 140
5
votes
3
replies
1.3k
views
Latent factors for differential expression
deseq2
zinbwave
10X
scRNA-seq
Differential expression
updated 3.7 years ago by
Michael Love
41k • written 3.7 years ago by
vincent.croset
▴ 20
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 3.7 years ago by
davide risso
▴ 950 • written 3.8 years ago by
Wagaa
▴ 10
0
votes
0
replies
632
views
clustering of scRNAseq gene expression at multiple time points
scRNA-seq
time series
3.7 years ago
Bogdan
▴ 670
2
votes
4
replies
913
views
scRNA-seq question, assayData() error
assayData()
scRNA-seq
single cell sequencing
assayData
Bioconductor
updated 3.8 years ago by
Kevin Blighe
★ 3.9k • written 3.8 years ago by
Wagaa
▴ 10
3
votes
6
replies
2.8k
views
Carry over variable features when converting FastMNN SCE object to Seurat object
mnn
batchelor
scrna-seq
seurat
updated 3.8 years ago by
Aaron Lun
★ 28k • written 3.8 years ago by
heir_of_isildur88
• 0
7
votes
3
replies
4.6k
views
Downsample or not to downsample?
scrna-seq
downsampleBatches
scran
updated 3.9 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
p.joshi
▴ 40
3
votes
11
replies
1.7k
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
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 4.2 years ago by
p.joshi
▴ 40
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 4.2 years ago by
heir_of_isildur88
• 0
4
votes
2
replies
713
views
scRNA-seq analysis : the IDENTITY of the CLUSTERS across MULTIPLE EXPERIMENTS
scRNA-seq
updated 4.2 years ago by
Aaron Lun
★ 28k • written 4.2 years ago by
Bogdan
▴ 670
1
vote
3
replies
1.2k
views
comparing 2 models with confounders with MAST (scRNA-seq DEA)
scRNA-seq
MAST
confounders
updated 4.2 years ago by
Andrew_McDavid
▴ 270 • written 4.2 years ago by
ramonmassoni
▴ 10
0
votes
0
replies
834
views
Job:
Bioinformatics Scientist, CNS Transcriptomics at Alnylam Pharmaceuticals, Cambridge MA, USA
scRNA-seq
CNS
transcriptomics
RNAi
Job
4.2 years ago
Joseph Barry
▴ 10
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
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
0
votes
1
reply
802
views
emptyDrops result is full NAs
scran
dropletUtils
scater
scRNA-Seq
4.8 years ago
hamza_karakurt
▴ 50
3
votes
3
replies
2.2k
views
edgeR: Strange volcano plot
edger
scRNA-seq
DGEA
updated 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
cronanz
• 0
4
votes
2
replies
2.2k
views
When to combine samples in the pre-processing of 10x scRNA-seq data?
10x
scrna-seq
updated 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
jma1991
▴ 70
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
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
1
vote
2
replies
1.3k
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
5
votes
5
replies
5.5k
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
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
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
★ 2.9k • written 5.1 years ago by
hamza_karakurt
▴ 50
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 19 months ago by
jamie.gearing
▴ 60 • written 5.1 years ago by
hamza_karakurt
▴ 50
2
votes
4
replies
2.2k
views
Silhouette Plots for Clustering Quality (Multiple Algorithm)
scRNA-Seq
RNA-Seq
Clustering
Silhouette Plot
updated 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
hamza_karakurt
▴ 50
0
votes
3
replies
1.4k
views
about scRNA-seq, SEURAT and CCA
scRNA-seq
updated 5.2 years ago by
James W. MacDonald
65k • written 5.2 years ago by
Bogdan
▴ 670
1
vote
1
reply
1.3k
views
gene counts in Seurat after RunCCA() and AlignSubspace()
scRNA-seq
seurat
CCA
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
Bogdan
▴ 670
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 5.3 years ago by
Steve Lianoglou
★ 13k • written 5.3 years ago by
Bogdan
▴ 670
0
votes
3
replies
1.3k
views
single cell RNA-seq pipeline
rnaseq
scRNA-seq
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
Bogdan
▴ 670
30 results • Page
1 of 1
Recent ...
Replies
Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
by
Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Votes
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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