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RNA seq
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reset
0
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9
replies
2.7k
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How to create manhattan plot with DESeq2
deseq2
mahattan plot
RNA Seq
updated 3.7 years ago by
bernatgel
▴ 150 • written 4.7 years ago by
adeler001
• 0
2
votes
5
replies
3.3k
views
Possible batch effect correction with RNA-Seq data when the batches do not contain both biological conditions for DE analysis
batch effect
limma
rna seq
DE
updated 4.2 years ago by
Steve Lianoglou
★ 13k • written 4.2 years ago by
svlachavas
▴ 830
0
votes
3
replies
677
views
Normalization of RNA seq data
RNA seq
cpm
updated 4.2 years ago by
Kevin Blighe
★ 3.9k • written 4.2 years ago by
isabel.pieterse
• 0
3
votes
3
replies
919
views
Custom gene annotations for SGSeq
sgseq
alternative splicing
rna seq
updated 4.6 years ago by
Leonard Goldstein
▴ 220 • written 4.6 years ago by
116100016
• 0
1
vote
4
replies
919
views
Difference between Fold Changes from EdgeR glmLRTest and directly calculated fold changes.
edger
RNA Seq
updated 4.6 years ago by
James W. MacDonald
66k • written 4.6 years ago by
abf
▴ 30
0
votes
0
replies
508
views
searching for specific RNA sequences
rna seq
4.6 years ago
adeler001
• 0
0
votes
2
replies
809
views
using only uniquely-mapping reads for alternative splicing using SGSeq
rna seq
SGSeq
Alternative splicing
updated 4.7 years ago by
Leonard Goldstein
▴ 220 • written 4.7 years ago by
116100016
• 0
0
votes
1
reply
564
views
51 views DESeq2 RNAseq differential expression analysis
deseq2
likelihood ratio
rna seq
wald test
updated 4.7 years ago by
Michael Love
42k • written 4.7 years ago by
adeler001
• 0
0
votes
2
replies
974
views
Need help cprrecting overlappinge genes on valcano plot
volcano plot
rna seq
updated 4.8 years ago by
Michael Love
42k • written 4.8 years ago by
adeler001
• 0
1
vote
5
replies
1.3k
views
Time course experiment using limma with voom
limma
voom
RNA Seq
Time-course experiments
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
mahes.muniandy
• 0
5
votes
3
replies
1.0k
views
Steep dendrograms and few modules. WGCNA on RNA seq data
RNA seq
wgcna
updated 5.0 years ago by
Peter Langfelder
★ 3.0k • written 5.0 years ago by
agustin.gonvi
▴ 20
1
vote
2
replies
1.9k
views
adapter trimming paired vs unpaired reads
rna seq
trimmomatic
trimming
adapter trimming
paired analysis
5.1 years ago
Mozart
▴ 30
0
votes
0
replies
1.6k
views
Sub clustering from hierarchical cluster used to make heat map of gene expression data
heatmap.2
hierarchical clustering
microarray
RNA seq
DEG
6.3 years ago
lawarde.ankita1
▴ 30
13 results • Page
1 of 1
Recent ...
Replies
Comment: gds in GEOmetadb 2023-06-26 version is empty
by
Frederico Moraes Ferreira
▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter
by
James W. MacDonald
66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat
by
Michael Love
42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Comment: Most enriched pathway is not expressed when modifying universe parameter
by
adripel
• 0
In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…
Answer: Design formula, numeric contrast, and lfcshrink in deseq2
by
Michael Love
42k
For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statist…
Votes
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
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