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RnaSeq
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Weird p-values using DESeq2?
DESeq2
RNASeq
updated 8 hours ago by
ATpoint
★ 4.7k • written 18 hours ago by
ingrid.h
• 0
0
votes
1
reply
105
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2
DifferentialExpression
DifferentialRegulation
RNASeq
GeneSetEnrichment
updated 3 days ago by
Michael Love
43k • written 7 days ago by
Sahil
• 0
0
votes
3
replies
328
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat
RNASeq
DESeq2
scRNAseq
updated 11 days ago by
jodan
• 0 • written 20 days ago by
Quang NN
▴ 10
0
votes
1
reply
130
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression
RNASeq
DESeq2
updated 16 days ago by
Michael Love
43k • written 17 days ago by
Sim
• 0
0
votes
2
replies
331
views
How to visualize these pathways using pathview
Salmo_salar
RNASeq
KEGG
pathview
17 days ago • updated 18 hours ago
ingrid.h
• 0
0
votes
4
replies
914
views
Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq
DESeq2
20 days ago • updated 17 days ago
Quang NN
▴ 10
0
votes
3
replies
508
views
DESeq2 analysis with transcript counts
Transcriptomics
RNASeq
DESeq2
written 5 weeks ago by
sindhuri
• 0
0
votes
5
replies
577
views
Identifying potentially associated gene set to drug response using GSVA
drug
RNASeq
GSVA
written 12 weeks ago by
Kent
• 0
1
vote
6
replies
6.6k
views
GSVA on RNAseq data
gsva
rnaseq
updated 2 days ago by
Robert Castelo
★ 3.4k • written 5.9 years ago by
rocanja
▴ 60
3
votes
5
replies
4.8k
views
plotMDS in edgeR
edger
rnaseq
written 9.4 years ago by
gthm
▴ 30
10 results • Page
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Answer: To count or not to count multi-overlapping reads?
by
Gordon Smyth
52k
> How does it handle reads that map to a gene that is located in a region that also has another gene but on the alternate strand? Overlapp…
Comment: Weird p-values using DESeq2?
by
ATpoint
★ 4.7k
This does not look like normalized counts but raw counts. Consider using `counts(dds, normalized = TRUE)` or the output of `normTransform()…
Answer: Weird p-values using DESeq2?
by
Wolfgang Huber
★ 13k
Dear Ingrid, thank you for asking. Can you provide the input count matrix (you can "pseudonymize" the biological conditions and the gene n…
Comment: How to visualize these pathways using pathview
by
ingrid.h
• 0
Yes I have seen it, thanks.
Comment: Store Matrix in DataFrame Cell
by
Dario Strbenac
★ 1.6k
It does not appear to work. > DataFrame(name = "test", value = list(matrix(1:4, ncol = 2))) DataFrame with 2 rows and 3 columns …
Votes
A: Fraction count for multi mapping reads; how to generate input file for Deseq2 fo
Comment: Weird p-values using DESeq2?
Comment: Overcoming confounding in batch effect correction
Answer: Store Matrix in DataFrame Cell
Answer: enrichGOgradient color change
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