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Biased results of DESeq2 LRT (Group name order)
deseq2 written 3 hours ago by minyoungcho93 • 0 • updated 3 hours ago by Michael Love ♦ 25k
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What is lfcSE and how is it calculated?
deseq2 standarderror written 12 hours ago by lizzid • 0
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Very variable samples vs similar samples in the same dataset
edger deseq2 written 13 hours ago by eduardogccm • 0
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How to create manhattan plot with DESeq2
deseq2 rna seq mahattan plot written 15 hours ago by adeler001 • 0 • updated 14 hours ago by Michael Love ♦ 25k
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Exclude interaction terms from the design
deseq2 statistics modelling written 17 hours ago by polyptwo • 0
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What are size factors used for in baseMean calculation
deseq2 written 1 day ago by lizzid • 0 • updated 1 day ago by Michael Love ♦ 25k
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How I deal with this expression set
deseq2 R written 1 day ago by jivarajivaraj • 10 • updated 1 day ago by Michael Love ♦ 25k
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DEseq2 loading library problem
deseq2 written 3 days ago by shilabr • 0 • updated 3 days ago by Martin Morgan ♦♦ 23k
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DESeq2 installation issue
deseq2 written 3 days ago by eric.trezel • 0 • updated 3 days ago by Martin Morgan ♦♦ 23k
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DESeq2 analysis with multiple factors
deseq2 deg multiplefactors written 3 days ago by yura.song • 0 • updated 3 days ago by Steve Lianoglou ♦ 12k
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DESeq2 - lfcShrink reversing sign for all logFCs - clarification on "contrast" argument?
deseq2 written 4 days ago by christopherlhartl • 0 • updated 4 days ago by Michael Love ♦ 25k
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write.table of DESeq2 results broken down by LFC
deseq2 written 4 days ago by rbronste • 60 • updated 4 days ago by Michael Love ♦ 25k
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Differential gene expression analysis
deseq2 written 4 days ago by rthapa • 0 • updated 4 days ago by Michael Love ♦ 25k
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Difference in PCA variance calculation in DESeq2
deseq2 hclust pca written 4 days ago by ag1805x • 20 • updated 4 days ago by Michael Love ♦ 25k
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tximeta link to transcriptome
deseq2 written 5 days ago by eric.blanc • 0 • updated 5 days ago by Michael Love ♦ 25k
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Paired t-test with DESeq2
deseq2 written 12 days ago by Mozart • 10 • updated 12 days ago by swbarnes2 • 330
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DESeq2: compare all tpts to baseline and pull results table accordingly
deseq2 design contrast written 13 days ago by luciest.rodriguez • 0
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DESeq2 using many cores despite parallel = FALSE
deseq2 parallel written 13 days ago by symbiologist • 0 • updated 13 days ago by Michael Love ♦ 25k
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Batch correction by using ComBat function in sva package
deseq2 combat tutorial knownbatcheffect written 14 days ago by rajeshparmar4 • 0 • updated 13 days ago by Yuqing Zhang • 20
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Modelling a multiplicative batch effect with DESeq2
deseq2 combat batch-effects written 14 days ago by Samuel • 0 • updated 13 days ago by Michael Love ♦ 25k
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Multiple samples per individual and unbalanced number of samples per individual: DE between groups still an ordinary two-group comparison?
limma edger deseq2 differential expression repeated measures written 15 days ago by hermidalc • 0
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DESeq2 VS edgeR DEG results different in analysis same data
edger deseq2 written 15 days ago by 15958021290 • 0 • updated 14 days ago by Gordon Smyth ♦ 39k
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Combining RSEM Files with dif row # for tximport
rnaseq deseq2 tximport written 15 days ago by venura • 0 • updated 15 days ago by Michael Love ♦ 25k
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Batch effects between different sequencing runs
deseq2 batchcorrection written 17 days ago by A • 40 • updated 17 days ago by swbarnes2 • 330
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DESeq2 lfcshrink generate 0 svalues
deseq2 written 17 days ago by corentin.lyon • 0 • updated 17 days ago by Michael Love ♦ 25k
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