Showing : degs • reset
5
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3
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29k
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DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 6.7 years ago by ▴ 30
0
votes
3
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1.0k
views
code syntax for DESeq2 to derive DEGs from a complicated contrast or interaction contrast?
DESeq2 Complicated.contrast DEGs
updated 3.0 years ago by 43k • written 3.1 years ago by • -60
-6
votes
4
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1.2k
views
is it possible and reasonable for edgeR to derive DEGs from a complicated contrast or contrast of contrast?
complicated.contrast edgeR DEGs
3.1 years ago Mike • -60
2
votes
3
replies
1.3k
views
Classic or GLM approach in edgeR, Why do I got less DEG in GLM approach?
edgeR DEGs
updated 3.5 years ago by 53k • written 3.5 years ago by • 0
0
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2
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1.2k
views
Extend comparisons between two groups to more groups in DESEQ2
edgeR DEGs DESEQ2 RNASeqData
3.6 years ago Raito92 ▴ 60
0
votes
3
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1.4k
views
EdgeR question: why I got discrepancy results for DEGs when using different ways setting up the models
RNAseq edgeR DEGs
updated 3.6 years ago by 53k • written 4.1 years ago by ▴ 380
0
votes
20
replies
3.5k
views
DESeq2 question: why I got discrepancy results for DEGs when using different ways setting up the models
DESeq2 DEGs
4.2 years ago • updated 4.1 years ago Ming ▴ 380
2
votes
1
reply
9.1k
views
EnhancedVolcano Label Question
RNASeq EnhancedVolcano DEGs
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by • 0
0
votes
2
replies
1.4k
views
Deseq2 cooks filter for 2 replicates x 3 replicates
DESeq2 Nullcook'svalues 2x3 DEGs
4.5 years ago andreia ▴ 10
4
votes
5
replies
2.0k
views
DEseq2 results
heatmaps DEGs PCA
updated 4.6 years ago by ★ 4.0k • written 4.6 years ago by • 0
2
votes
2
replies
1.4k
views
Design formula for pairwise comparison of experimental setup with multiple factors
DEGs DESeq2
4.7 years ago 2021yearsold • 0
0
votes
1
reply
1.2k
views
mircomb analysis from deg's list
mircomb mrna mirna degs interaction
5.2 years ago andreia ▴ 10
0
votes
2
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1.1k
views
mirna-mrna interation mircomb (from DEGs and DEMs lists)
deseq2 mircomb degs dems
updated 5.2 years ago by 43k • written 5.2 years ago by ▴ 10
0
votes
1
reply
1.2k
views
compareCluster error: On clusterProfiler DEGs enrichments analysis
clusterProfiler Bioconductor R DEGs
5.3 years ago tpm • 0
3
votes
2
replies
3.6k
views
How to deal with elimination of genes when using filterByExpr function?
edger DEGs normalization
updated 5.7 years ago by 53k • written 5.7 years ago by ▴ 10
2
votes
4
replies
1.4k
views
How to make grouping and contrast for multfactor design?
edger DEGs
5.7 years ago anikng ▴ 10
2
votes
3
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1.5k
views
How to correctly set up the design in DESeq2 for RRPP?
deseq2 rrpp DEGs RNAseq
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
votes
2
replies
5.3k
views
Heatmap of selected genes
heatmap DEGs RNAseq DESeq2
updated 6.2 years ago by ▴ 280 • written 6.2 years ago by • 0
4
votes
3
replies
1.6k
views
Differential profile for only one normal - tumor pair
edger degs paired design
updated 7.2 years ago by 53k • written 7.2 years ago by ▴ 10
3
votes
5
replies
2.7k
views
DEGs of microarray Data and hierarchical clustering and visualizing using heatmap
limma heatmap DEGs
updated 7.7 years ago by 53k • written 7.7 years ago by ▴ 30
3
votes
1
reply
1.4k
views
Common dispersion value using edgeR for DEGs analysis
edgeR DEGS common disperion
updated 8.1 years ago by ★ 29k • written 8.1 years ago by • 0
6
votes
4
replies
3.4k
views
Identification of DEGs through limma analysis
limma microarray DEGs p values lfc
8.3 years ago rkp • 0
22 results • Page 1 of 1
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Comment: Sharing a collection of datasets in ExperimentHub by Peter Hickey ▴ 760
The [**scRNAseq**](https://bioconductor.org/packages/scRNAseq/) package ([source on GitHub](https://github.com/LTLA/scRNAseq)) might serve …
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi by ReinholdGaylord99 • 0
Thank you so much! https://www.nature.com/articles/s41467-021-25960-2/ [geometry dash lite](https://geometrydashlite.online)
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k
I'm not sure that I understand. You have a dataset that, even after pseudo-bulking, still has 6000 samples? That is surprising. Retaining …
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by abaed • 0
Hello again @gordonsmyth, I've now applied the analysis using a more detailed annotation of cell types/clusters, which includes about 100 …
Answer: Sharing a collection of datasets in ExperimentHub by shepherl 4.2k
107 packages would be a lot! It is certainly possible (and recommended) to implement one package that utilizes ExperimentHub for controlli…
Votes
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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