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fishpond
•
reset
2
votes
2
replies
2.0k
views
Volcano plots of DEGs from Swish are weird
DESeq2
fishpond
salmon
swish
2.6 years ago
Qin
▴ 10
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
41k • 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
41k • written 3.0 years ago by
Jack Riley
• 0
0
votes
8
replies
1.4k
views
swish in a blocking design?
fishpond
swish
2.2 years ago
msll0802
• 0
1
vote
3
replies
1.4k
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon
rna-seq
swish
bootstrap
fishpond
updated 2.2 years ago by
Michael Love
41k • written 2.2 years ago by
samuelcjx
• 0
0
votes
8
replies
1.3k
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
3.5 years ago
thomas.dugedebernonville
• 0
3
votes
5
replies
1.3k
views
Swish (fishpond) scaled counts result
Swish
fishpond
3.2 years ago
675743
▴ 20
4
votes
7
replies
1.0k
views
Fishpond/Swish Interaction Test Error
fishpond
swish
10 months ago
Miguel
▴ 20
1
vote
3
replies
1.0k
views
Swish: contrasts and interactions
fishpond
DESeq2
updated 12 months ago by
Michael Love
41k • written 21 months ago by
alexyz
• 0
1
vote
2
replies
1.0k
views
Swish direction of comparison based on order of factors
fishpond
2.6 years ago
Jean
• 0
1
vote
1
reply
1000
views
Swish with more than two conditions. Add support for contrasts?
tximeta
DESeq2
swish
fishpond
updated 2.3 years ago by
Michael Love
41k • written 2.3 years ago by
jeremymsimon
▴ 20
3
votes
2
replies
869
views
the result of swish function from fishpond package
fishpond
swish
updated 3.9 years ago by
Michael Love
41k • written 3.9 years ago by
1911449
• 0
1
vote
3
replies
795
views
collapseReplicates error after tximeta
fishpond
tximeta
DESeq2
updated 7 months ago by
Michael Love
41k • written 15 months ago by
Rihards Saksis
• 0
0
votes
3
replies
676
views
Fishpond with unbalanced dataset
rna-seq
salmon
fishpond
swish
updated 10 months ago by
Michael Love
41k • written 10 months ago by
samuelcjx
• 0
0
votes
3
replies
300
views
Interaction tests and paired interaction tests in swish
swish
salmon
fishpond
updated 3 months ago by
Michael Love
41k • written 3 months ago by
Nicholas
• 0
16 results • Page
1 of 1
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Answer: SGSeq: moving toward diffex from SGSeq analysis
by
Leonard Goldstein
▴ 200
`vid` and `eid` are unique identifiers for splice variants and splicing events respectively. They are analogous to exon bin and gene identi…
Comment: Help with error using camera() in limma
by
Chris
• 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size
by
XW
• 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Comment: Limma, eBayes different sample size of groups and adjustment
by
XW
• 0
Could you explain more about how the analysis self-correct the different sample sizes when calling DEGs in limma? Thanks
Answer: How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
by
James W. MacDonald
65k
The section of the vignette that is *directly above the one you quote* says that you can use the HMMcopy utils to do all three things. And …
Votes
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
Comment: Help with error using camera() in limma
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