Showing : fishpond • reset
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Curiously shaped volcano plot with using oarfish + swish to do differential gene expression on long-read RNA-seq
fishpond fish
updated 3 months ago by 43k • written 3 months ago by • 0
0
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11
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913
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Problems with oarfish + tximport + swish
fishpond tximport tximeta
updated 3 months ago by • 0 • written 3 months ago by • 0
1
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1
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536
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Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 3 months ago by 43k • written 3 months ago by • 0
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3
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754
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Interaction tests and paired interaction tests in swish
swish salmon fishpond
updated 15 months ago by 43k • written 15 months ago by • 0
4
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7
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1.4k
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Fishpond/Swish Interaction Test Error
fishpond swish
22 months ago Miguel ▴ 20
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3
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1.0k
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Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 22 months ago by 43k • written 22 months ago by • 0
1
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3
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1.2k
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collapseReplicates error after tximeta
fishpond tximeta DESeq2
updated 19 months ago by 43k • written 2.2 years ago by • 0
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3
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1.5k
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Swish: contrasts and interactions
fishpond DESeq2
updated 2.0 years ago by 43k • written 2.7 years ago by • 0
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8
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1.8k
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Swish log2FC NA output
swish fishpond DifferentialExpression
2.7 years ago jvandinter • 0
5
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9
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2.1k
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Questions regarding failing tximeta import for swish
swish fishpond GenomicFeatures tximeta
updated 2.7 years ago by 43k • written 3.0 years ago by • 0
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8
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1.9k
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swish in a blocking design?
fishpond swish
3.2 years ago msll0802 • 0
1
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3
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1.9k
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Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
1
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1
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1.4k
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Swish with more than two conditions. Add support for contrasts?
tximeta DESeq2 swish fishpond
updated 3.2 years ago by 43k • written 3.2 years ago by ▴ 20
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2
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1.4k
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Swish direction of comparison based on order of factors
fishpond
3.6 years ago Jean • 0
2
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2
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2.9k
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Volcano plots of DEGs from Swish are weird
DESeq2 fishpond salmon swish
3.6 years ago Qin ▴ 10
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6
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1.9k
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Running swish on a non-reference transcript assembly / tximeta import issue
tximeta swish fishpond
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
3
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5
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1.8k
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Swish (fishpond) scaled counts result
Swish fishpond
4.2 years ago • updated 4.1 years ago 675743 ▴ 20
3
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6
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1.7k
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Swish with covariate for batch effect
swish fishpond
4.5 years ago thomas.dugedebernonville • 0
3
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2
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1.1k
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the result of swish function from fishpond package
fishpond swish
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
19 results • Page 1 of 1
Recent ...
Replies
Comment: RNA Seq using Lrt by Rob • 0
So if I have understood what you have said : If i want to see if Day (time) has an effect / is being tested - then the reduced model should…
Comment: How to convert transcript counts to gene counts in R? by ben • 0
Simply summing transcripts by gene is sufficient for use with DESeq2. [sprunki clicker][1] [1]: https://sprunkiclicker.com/
Answer: EuroBioC2024 abstract submission is open! by Ali • 0
[Promo products][1] are a smart way to boost visibility, especially with exciting updates like *News: EuroBioC2024 abstract submission is o…
Answer: ROAST for small sets by Gordon Smyth 52k
The p-values from `mroast` will be the same (up to sampling variability associated with random rotations) regardless of whether you test al…
Comment: FlowSOM library requires igraph but igraph does not install by Szabolcs • 0
The R/igraph Installation FAQ covers most issues: https://r.igraph.org/articles/installation-troubleshooting.html
Votes
Answer: ROAST for small sets
Answer: ROAST for small sets
A: conceptual question about FDR, FDR adjusted p-value and q-value
Comment: edgeR::cpm() results in negative values from raw counts of 0
Comment: edgeR::cpm() results in negative values from raw counts of 0
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