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Scrna
•
reset
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
4
votes
3
replies
1.0k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq
scrna
paireddesign
edgeR
pseudobulking
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
garcia
• 0
2
votes
13
replies
2.3k
views
Running the DESeq2 "DESeqDataSetFromMatrix" function returns a dimname error
DESeq2
Scrna
scRNAseq
2.8 years ago
RDoc
▴ 10
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
1
reply
1.0k
views
Combining treatment and control batches for analysis
scRNAseq
scRNA
batchelor
BatchEffect
updated 3.5 years ago by
Aaron Lun
★ 28k • written 3.5 years ago by
Adrien
• 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
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
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
1
vote
2
replies
795
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq
quickcluster
scRNA
scran
4 months ago
ruba-mahmoud
• 0
1
vote
0
replies
668
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
0
votes
1
reply
894
views
DeSeq2 , Differntial expression
SCRNA
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
sumetha
• 0
0
votes
2
replies
679
views
Could not find function "Standard Chromosomes"
scrna
scRNAseq
updated 6 months ago by
Gabriella
• 0 • written 14 months ago by
sarah.jobbins
• 0
0
votes
1
reply
416
views
If highly-expressed genes are upregulated, what happens to genes with lower expression after normalization?
scRNA
scRNAseq
updated 9 months ago by
ATpoint
★ 4.1k • written 9 months ago by
Omer
• 0
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
15 results • Page
1 of 1
Recent ...
Replies
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
> I am just re-processing due to being uncertain about how they used the edgeR analysis to reach gene level edgeR devs published something…
Comment: Differences in differential analysis methods for RNA-Seq
by
james.zhang20
• 0
Thanks for the explanations, it has helped clarify some things. Unfortunately, I am working from an early access public dataset (https://do…
Comment: Deseq2 and Normalization of RNA sequencing data
by
ATpoint
★ 4.1k
There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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