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pseudobulk
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1.4k
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DESeq2 aggregated single cell data
pseudobulk
SingleCell
DESeq2
21 months ago
fluentin44
• 0
2
votes
0
replies
1.1k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk
scRNAseq
GSVA
12 months ago
Tadeoye
▴ 20
0
votes
3
replies
856
views
Tissue Level Differential Expression Analysis
DESeq2
DifferentialExpression
differentialex
Pseudobulk
SingleCell
updated 16 months ago by
Michael Love
41k • written 16 months ago by
skanda.hebbale
• 0
0
votes
5
replies
799
views
scRNA-seq as pseudobulk for DEseq2: does AggregateExpression() normalize counts?
pseudobulk
seurat
DESeq2
updated 4 months ago by
Kevin Blighe
★ 3.9k • written 4 months ago by
daiane.hemerichbrennan
• 0
3
votes
4
replies
415
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk
edgeR
DifferentialExpression
updated 8 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
Jack S.
▴ 50
0
votes
1
reply
379
views
Pseudobulk-DESeq2 analyze multiple cell types at once?
pseudobulk
DESeq2
updated 10 weeks ago by
Michael Love
41k • written 10 weeks ago by
puffsquash
• 0
6 results • Page
1 of 1
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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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