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swish
•
reset
2
votes
2
replies
2.1k
views
Volcano plots of DEGs from Swish are weird
DESeq2
fishpond
salmon
swish
2.7 years ago
Qin
▴ 10
1
vote
3
replies
1.7k
views
miRNA differential expression analysis - treat as transcript level?
tximport
DESeq2
edgeR
swish
miRNA
updated 23 months ago by
Michael Love
42k • written 23 months ago by
BG
• 0
5
votes
9
replies
1.6k
views
Questions regarding failing tximeta import for swish
swish
fishpond
GenomicFeatures
tximeta
updated 21 months ago by
Michael Love
42k • written 2.1 years ago by
jvandinter
• 0
0
votes
6
replies
1.4k
views
Running swish on a non-reference transcript assembly / tximeta import issue
tximeta
swish
fishpond
updated 3.0 years ago by
Michael Love
42k • written 3.1 years ago by
Jack Riley
• 0
1
vote
3
replies
1.4k
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon
rna-seq
swish
bootstrap
fishpond
updated 2.3 years ago by
Michael Love
42k • written 2.3 years ago by
samuelcjx
• 0
0
votes
8
replies
1.4k
views
swish in a blocking design?
fishpond
swish
2.2 years ago
msll0802
• 0
0
votes
8
replies
1.4k
views
Swish log2FC NA output
swish
fishpond
DifferentialExpression
21 months ago
jvandinter
• 0
3
votes
6
replies
1.3k
views
Swish with covariate for batch effect
swish
fishpond
3.6 years ago
thomas.dugedebernonville
• 0
3
votes
5
replies
1.3k
views
Swish (fishpond) scaled counts result
Swish
fishpond
3.3 years ago • updated 3.2 years ago
675743
▴ 20
4
votes
7
replies
1.1k
views
Fishpond/Swish Interaction Test Error
fishpond
swish
11 months ago
Miguel
▴ 20
1
vote
1
reply
1.0k
views
Swish with more than two conditions. Add support for contrasts?
tximeta
DESeq2
swish
fishpond
updated 2.3 years ago by
Michael Love
42k • written 2.3 years ago by
jeremymsimon
▴ 20
3
votes
2
replies
881
views
the result of swish function from fishpond package
fishpond
swish
updated 3.9 years ago by
Michael Love
42k • written 3.9 years ago by
1911449
• 0
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
0
votes
3
replies
321
views
Interaction tests and paired interaction tests in swish
swish
salmon
fishpond
updated 3 months ago by
Michael Love
42k • written 3 months ago by
Nicholas
• 0
14 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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