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DEGS
•
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0
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20
replies
2.3k
views
DESeq2 question: why I got discrepancy results for DEGs when using different ways setting up the models
DESeq2
DEGs
2.7 years ago
Ming
▴ 380
4
votes
5
replies
1.3k
views
DEseq2 results
heatmaps
DEGs
PCA
updated 3.1 years ago by
Kevin Blighe
★ 3.9k • written 3.1 years ago by
MOHAMMAD
• 0
3
votes
5
replies
2.0k
views
DEGs of microarray Data and hierarchical clustering and visualizing using heatmap
limma
heatmap
DEGs
updated 6.2 years ago by
Gordon Smyth
50k • written 6.2 years ago by
lawarde.ankita1
▴ 30
6
votes
4
replies
2.6k
views
Identification of DEGs through limma analysis
limma
microarray
DEGs
p values
lfc
6.8 years ago
rkp
• 0
2
votes
4
replies
950
views
How to make grouping and contrast for multfactor design?
edger
DEGs
4.2 years ago
anikng
▴ 10
-6
votes
4
replies
813
views
is it possible and reasonable for edgeR to derive DEGs from a complicated contrast or contrast of contrast?
complicated.contrast
edgeR
DEGs
19 months ago
Mike
• -60
2
votes
3
replies
870
views
Classic or GLM approach in edgeR, Why do I got less DEG in GLM approach?
edgeR
DEGs
updated 2.0 years ago by
Gordon Smyth
50k • written 2.0 years ago by
RR
• 0
2
votes
3
replies
932
views
How to correctly set up the design in DESeq2 for RRPP?
deseq2
rrpp
DEGs
RNAseq
updated 4.4 years ago by
Michael Love
41k • written 4.4 years ago by
gmchaput
• 0
4
votes
3
replies
1.1k
views
Differential profile for only one normal - tumor pair
edger
degs
paired design
updated 5.7 years ago by
Gordon Smyth
50k • written 5.7 years ago by
takumima
▴ 10
0
votes
3
replies
922
views
EdgeR question: why I got discrepancy results for DEGs when using different ways setting up the models
RNAseq
edgeR
DEGs
updated 2.1 years ago by
Gordon Smyth
50k • written 2.6 years ago by
Ming
▴ 380
0
votes
3
replies
598
views
code syntax for DESeq2 to derive DEGs from a complicated contrast or interaction contrast?
DESeq2
Complicated.contrast
DEGs
updated 18 months ago by
Michael Love
41k • written 18 months ago by
Mike
• -60
0
votes
2
replies
4.0k
views
Heatmap of selected genes
heatmap
DEGs
RNAseq
DESeq2
updated 4.7 years ago by
mikhael.manurung
▴ 270 • written 4.7 years ago by
danikadigiacomo
• 0
3
votes
2
replies
2.3k
views
How to deal with elimination of genes when using filterByExpr function?
edger
DEGs
normalization
updated 4.2 years ago by
Gordon Smyth
50k • written 4.2 years ago by
anikng
▴ 10
0
votes
2
replies
761
views
mirna-mrna interation mircomb (from DEGs and DEMs lists)
deseq2
mircomb
degs
dems
updated 3.7 years ago by
Michael Love
41k • written 3.7 years ago by
andreia
▴ 10
2
votes
2
replies
982
views
Design formula for pairwise comparison of experimental setup with multiple factors
DEGs
DESeq2
3.2 years ago
2021yearsold
• 0
0
votes
2
replies
932
views
Deseq2 cooks filter for 2 replicates x 3 replicates
DESeq2
Nullcook'svalues
2x3
DEGs
3.0 years ago
andreia
▴ 10
0
votes
2
replies
741
views
Extend comparisons between two groups to more groups in DESEQ2
edgeR
DEGs
DESEQ2
RNASeqData
2.2 years ago • updated 2.1 years ago
Raito92
▴ 60
5
votes
2
replies
21k
views
DESeq2: thousands of NA for pvalues?
deseq2
rna-seq
DEGs
cooks cutoff
updated 2.2 years ago by
rickap
• 0 • written 5.2 years ago by
aishu.jp
▴ 30
0
votes
1
reply
860
views
compareCluster error: On clusterProfiler DEGs enrichments analysis
clusterProfiler
Bioconductor
R
DEGs
3.8 years ago
tpm
• 0
2
votes
1
reply
4.5k
views
EnhancedVolcano Label Question
RNASeq
EnhancedVolcano
DEGs
updated 2.8 years ago by
Kevin Blighe
★ 3.9k • written 2.8 years ago by
robledoj13
• 0
3
votes
1
reply
1.1k
views
Common dispersion value using edgeR for DEGs analysis
edgeR
DEGS
common disperion
updated 6.6 years ago by
Aaron Lun
★ 28k • written 6.6 years ago by
baus87
• 0
0
votes
1
reply
795
views
mircomb analysis from deg's list
mircomb
mrna
mirna
degs
interaction
3.8 years ago • updated 3.7 years ago
andreia
▴ 10
22 results • Page
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Comment: limma models out of memory issue on Slurm HPC
by
SamGG
▴ 330
> Alternatively you could run each linear model fit (var1 to var6) in a separate batch run, and again that would presumably work. I think …
Comment: fgsea fork
by
shepherl
3.8k
For What its worth BiocManager should also be able to install the github remotes `BiocManager::install("ctlab/fgsea")`
Comment: fgsea fork
by
alserg
▴ 240
I'm also not sure what you mean by fork, but you also can install the latest version of fgsea directly from GitHub with `devtools::install_…
Comment: limma models out of memory issue on Slurm HPC
by
Jitendra
▴ 10
thanks Gordon, but our methylation epic array input file is quite big and we can't read it in R by just using laptop memory so we need to …
Comment: Doing comparison of RNA-seq data using EdgeR
by
Michael Love
41k
Just to clarify, when I originally posted the title and tags had listed "DESeq2" and then the post was changed after my answer was added. …
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
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
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