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DEseq2
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DESeq2 filtering vs edgeR filtering
DESeq2
15 days ago • updated 2 days ago
fr8712ca-s
• 0
0
votes
3
replies
159
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PCA of different bacterial species
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
Laura
▴ 10
1
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2
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134
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DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
7 days ago • updated 1 day ago
Chanderkant Chaudhary
• 0
3
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2
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118
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How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2
Transcriptomics
3 days ago
Anita
▴ 10
0
votes
1
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88
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collapseReplicates dimension error
DESeq2
Dese
updated 2 days ago by
Michael Love
41k • written 6 days ago by
Léa
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23
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New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 2 hours ago by
Michael Love
41k • written 3 hours ago by
Mikushi
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Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
by
Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
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A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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