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scrna
•
reset
1
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2
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ScRNAseq analysis scran :: quickcluster Error
scRNAseq
quickcluster
scRNA
scran
4 months ago
ruba-mahmoud
• 0
0
votes
2
replies
671
views
Could not find function "Standard Chromosomes"
scrna
scRNAseq
updated 6 months ago by
Gabriella
• 0 • written 13 months ago by
sarah.jobbins
• 0
4
votes
3
replies
1.0k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq
scrna
paireddesign
edgeR
pseudobulking
updated 8 months ago by
Gordon Smyth
50k • written 8 months ago by
garcia
• 0
0
votes
1
reply
411
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 9 months ago by
Omer
• 0
1
vote
0
replies
658
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran
Normalization
scRNA
BatchEffect
16 months ago
r_grau
▴ 10
4
votes
5
replies
2.3k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils
emptyDrops
scRNA
scRNAseq
10x
21 months ago • updated 20 months ago
Peter Hickey
▴ 740
2
votes
13
replies
2.2k
views
Running the DESeq2 "DESeqDataSetFromMatrix" function returns a dimname error
DESeq2
Scrna
scRNAseq
2.8 years ago
RDoc
▴ 10
1
vote
1
reply
997
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
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 3.6 years ago by
davide risso
▴ 950 • written 3.6 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
3
replies
1.7k
views
Error: no applicable method for `RunTSNE` applied to an object of class "try-error"
Seurat
scRNA
debugging
exceptions
unit-test
updated 4.5 years ago by
Martin Morgan
25k • written 4.5 years ago by
moldach
▴ 20
0
votes
1
reply
4.6k
views
monocle error at orderCells
scRNA
monocle
packages
Tutorial
4.7 years ago
444579004
• 0
1
vote
3
replies
1.5k
views
Differential Expression analysis between distinct scRNA-seq datasets
scrna
scrnaseq
differential gene expression
updated 6.5 years ago by
davide risso
▴ 950 • written 6.5 years ago by
d.depledge
• 0
0
votes
1
reply
890
views
DeSeq2 , Differntial expression
SCRNA
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
sumetha
• 0
2
votes
1
reply
4.2k
views
Intepretation of Z scores for gene set enrichment analysis in MAST
MAST
scRNA
GSEA
updated 6.8 years ago by
Andrew_McDavid
▴ 270 • written 6.8 years ago by
siajunren
• 0
1
vote
2
replies
1.5k
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
15 results • Page
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Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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