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RNA-seq
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53
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2
PCAplot
RNA-Seq
DesignModel
18 hours ago • updated 17 hours ago
shaunpeterson
• 0
1
vote
2
replies
258
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
9 days ago • updated 8 days ago
Dylan.Sheerin
• 0
2
votes
3
replies
254
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 13 days ago by
ATpoint
★ 4.1k • written 14 days ago by
Reza
• 0
3
votes
3
replies
368
views
permutation test in edgeR
rna-seq
edgeR
updated 27 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Netanel
• 0
0
votes
1
reply
917
views
Human genes correlation to Bacterial genes
correlation
pearsoncorrelation
rna-seq
differential gene expression
updated 5 months ago by
ATpoint
★ 4.1k • written 6.1 years ago by
saad_k6
• 0
0
votes
2
replies
324
views
WGCNA less samples
RNA-Seq
WGCNA
Worms
5 months ago
davca
• 0
0
votes
4
replies
733
views
DESeq2 : standardising variation between treatments
RNA-seq
DESeq2
7 months ago
ar14g12
• 0
0
votes
2
replies
3.5k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq
featureCounts
ht-seq
written 3.8 years ago by
ag1805x
▴ 80
2
votes
3
replies
1.7k
views
TPM from STAR mapped counts
GeneExpression
GenomicFeatures
RNA-Seq
TPM
updated 8 months ago by
Gordon Smyth
50k • written 8 months ago by
gingergeiger22
• 0
0
votes
3
replies
689
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq
RNA-seq
DESeq2
updated 8 months ago by
Alejandro Reyes
★ 1.9k • written 8 months ago by
Alice
• 0
3
votes
4
replies
892
views
lfcShrink() and batch effects in DESeq2
BatchEffect
lfcshrink
RNA-seq
DESeq2
9 months ago
Eva
▴ 10
0
votes
3
replies
710
views
Fishpond with unbalanced dataset
rna-seq
salmon
fishpond
swish
updated 11 months ago by
Michael Love
42k • written 11 months ago by
samuelcjx
• 0
5
votes
7
replies
1.2k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering
RNA-Seq
CPM
edgeR
filterByExpr
updated 11 months ago by
Gordon Smyth
50k • written 11 months ago by
mohammedtoufiq91
▴ 10
0
votes
2
replies
2.3k
views
Incorporating spike-ins to rna-seq analysis
Spike-in
RNASeqR
DESeq2
Normalization
rna-seq
updated 8 months ago by
manuel.fernandez
• 0 • written 2.1 years ago by
cicely.day
• 0
0
votes
10
replies
2.3k
views
Error in reading data on isoformswitchanalyzeR
isoformswitchanalyzeR
rna-seq
splice-variants
written 5.1 years ago by
saddamhusain77
• 0
9
votes
12
replies
7.9k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 29 days ago by
Elizabeth
• 0 • written 8.9 years ago by
gthm
▴ 30
16 results • Page
1 of 1
Recent ...
Replies
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
JKim
• 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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