Showing : fishpond • reset
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477
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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 9 months ago by 43k • written 9 months ago by • 0
0
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11
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1.4k
views
Problems with oarfish + tximport + swish
fishpond tximport tximeta
updated 9 months ago by • 0 • written 9 months ago by • 0
1
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1
reply
862
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Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 10 months ago by 43k • written 10 months ago by • 0
0
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3
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950
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Interaction tests and paired interaction tests in swish
swish salmon fishpond
updated 21 months ago by 43k • written 21 months ago by • 0
4
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7
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1.6k
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Fishpond/Swish Interaction Test Error
fishpond swish
2.4 years ago Miguel ▴ 20
0
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3
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1.2k
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Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
1
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3
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1.4k
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collapseReplicates error after tximeta
fishpond tximeta DESeq2
updated 2.1 years ago by 43k • written 2.8 years ago by • 0
1
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3
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1.6k
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Swish: contrasts and interactions
fishpond DESeq2
updated 2.5 years ago by 43k • written 3.3 years ago by • 0
0
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8
replies
2.1k
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Swish log2FC NA output
swish fishpond DifferentialExpression
3.3 years ago jvandinter • 0
5
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9
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2.4k
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Questions regarding failing tximeta import for swish
swish fishpond GenomicFeatures tximeta
updated 3.3 years ago by 43k • written 3.6 years ago by • 0
0
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8
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2.1k
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swish in a blocking design?
fishpond swish
3.7 years ago msll0802 • 0
1
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3
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2.2k
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Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
1
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1
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1.6k
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Swish with more than two conditions. Add support for contrasts?
tximeta DESeq2 swish fishpond
updated 3.8 years ago by 43k • written 3.8 years ago by ▴ 20
1
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2
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1.5k
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Swish direction of comparison based on order of factors
fishpond
4.1 years ago Jean • 0
2
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2
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3.1k
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Volcano plots of DEGs from Swish are weird
DESeq2 fishpond salmon swish
4.2 years ago • updated 4.1 years ago Qin ▴ 10
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6
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2.1k
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Running swish on a non-reference transcript assembly / tximeta import issue
tximeta swish fishpond
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
3
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5
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1.9k
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Swish (fishpond) scaled counts result
Swish fishpond
4.8 years ago • updated 4.7 years ago 675743 ▴ 20
3
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6
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1.9k
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Swish with covariate for batch effect
swish fishpond
5.1 years ago thomas.dugedebernonville • 0
3
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2
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1.3k
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the result of swish function from fishpond package
fishpond swish
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
19 results • Page 1 of 1
Recent ...
Replies
Answer: Integration: Paired-end vs healthy single-end from a different source by wba64023 • 0
Interesting comparison! The source differences can definitely impact read quality and bias. Curious to see how you handle normalization bet…
Comment: Could we detect difference at pathway level but not significant different at gen by wba64023 • 0
thanks for sharing! [slope 2][1] [1]: https://slope2.online
Comment: After running samtools, the featureCounts command crashed. by eja.gssssse.r.m • 0
The buffer overflow detected error in your featureCount step usually indicates that the program is trying to write more data into memory …
Comment: gene Set with high AUC score but no cells assigned to cell type by eja.gssssse.r.m • 0
It sounds like your AUCell results may be showing high AUC scores without cell assignment due to thresholding or scoring cutoffs. Think of …
Answer: "Watched Tags" are being erased rather than updated by shepherl 4.2k
This should now be resolved
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Bioconductor 3.22 Released!
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
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