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scRNA
•
reset
2
votes
13
replies
2.2k
views
Running the DESeq2 "DESeqDataSetFromMatrix" function returns a dimname error
DESeq2
Scrna
scRNAseq
2.7 years ago
RDoc
▴ 10
4
votes
5
replies
2.1k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils
emptyDrops
scRNA
scRNAseq
10x
20 months ago • updated 19 months ago
Peter Hickey
▴ 670
1
vote
4
replies
1.7k
views
How to work with duplicates calculating the differentially expressed genes in PseudoBulk-singleCell RNA experiment using zinbwave?
scRNA
zinbwave
batch
IntegratedData
updated 3.5 years ago by
davide risso
▴ 950 • written 3.5 years ago by
Assa Yeroslaviz
★ 1.5k
4
votes
3
replies
982
views
Custom design for scRNA DGE with pseudobulking
scRNAseq
scrna
paireddesign
edgeR
pseudobulking
updated 7 months ago by
Gordon Smyth
50k • written 7 months ago by
garcia
• 0
1
vote
3
replies
1.4k
views
Differential Expression analysis between distinct scRNA-seq datasets
scrna
scrnaseq
differential gene expression
updated 6.4 years ago by
davide risso
▴ 950 • written 6.4 years ago by
d.depledge
• 0
0
votes
3
replies
1.6k
views
Error: no applicable method for `RunTSNE` applied to an object of class "try-error"
Seurat
scRNA
debugging
exceptions
unit-test
updated 4.4 years ago by
Martin Morgan
25k • written 4.4 years ago by
moldach
▴ 20
1
vote
2
replies
1.4k
views
sc-RNA data analysis using scater
scater
scrna
updated 7.2 years ago by
Aaron Lun
★ 28k • written 7.2 years ago by
hrishi27n
▴ 20
1
vote
2
replies
627
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq
quickcluster
scRNA
scran
3 months ago
ruba-mahmoud
• 0
0
votes
2
replies
632
views
Could not find function "Standard Chromosomes"
scrna
scRNAseq
updated 5 months ago by
Gabriella
• 0 • written 12 months ago by
sarah.jobbins
• 0
0
votes
1
reply
869
views
DeSeq2 , Differntial expression
SCRNA
updated 6.4 years ago by
Aaron Lun
★ 28k • written 6.4 years ago by
sumetha
• 0
2
votes
1
reply
4.1k
views
Intepretation of Z scores for gene set enrichment analysis in MAST
MAST
scRNA
GSEA
updated 6.7 years ago by
Andrew_McDavid
▴ 270 • written 6.7 years ago by
siajunren
• 0
0
votes
1
reply
367
views
If highly-expressed genes are upregulated, what happens to genes with lower expression after normalization?
scRNA
scRNAseq
updated 8 months ago by
ATpoint
★ 4.0k • written 8 months ago by
Omer
• 0
1
vote
1
reply
948
views
Combining treatment and control batches for analysis
scRNAseq
scRNA
batchelor
BatchEffect
updated 3.4 years ago by
Aaron Lun
★ 28k • written 3.4 years ago by
Adrien
• 0
0
votes
1
reply
4.5k
views
monocle error at orderCells
scRNA
monocle
packages
Tutorial
4.6 years ago
444579004
• 0
1
vote
0
replies
592
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran
Normalization
scRNA
BatchEffect
15 months ago
r_grau
▴ 10
15 results • Page
1 of 1
Recent ...
Replies
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…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Comment: DEG Filtering
by
Gordon Smyth
50k
I already know that you using CEL files because you need them to perform RMA normalization. Yes, you should follow the advice I have alread…
Votes
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
Answer: error in ChAMP loading file
Circumvent creating .ff files in the working directory when using genotype.Illumina() function
Answer: Problem with maplot {affy} method when using rma {affy} method output as its inp
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