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Collapse Technical Replicates and Group-specific condition effects, individuals nested within groups
rnaseq deseq2 model.matrix collapsetechnicalreplicates written 12 hours ago by rbenel • 0 • updated 11 hours ago by Michael Love ♦ 26k
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tximeta error in fetching genome info
rnaseq tximeta written 1 day ago by MT • 0 • updated 1 day ago by Michael Love ♦ 26k
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Understanding voom behavior when model matrix is used with/without intercept for a continuous variable
rnaseq limma voom model.matrix intercept written 6 days ago by atakanekiz • 30 • updated 6 days ago by Gordon Smyth ♦ 39k
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DESeq2 counts function not working
rnaseq deseq deseq2 written 7 days ago by mrfossl97 • 0 • updated 7 days ago by Michael Love ♦ 26k
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JunctionSeq producing strangely large effect sizes for certain exon counting bins
rnaseq dexseq splicing junctionseq written 8 days ago by stuart • 10
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Can tximport be used to mitigate sample specific length biases?
rnaseq tximport written 19 days ago by abf • 0 • updated 19 days ago by Michael Love ♦ 26k
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How to correctly set up the design in DESeq2 for RRPP?
rnaseq deseq2 degs rrpp written 20 days ago by gmchaput • 0 • updated 20 days ago by Michael Love ♦ 26k
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RNAseq read counts generated by FeatureCounts
rnaseq featurecounts written 21 days ago by adeler001 • 0 • updated 21 days ago by James W. MacDonald ♦ 52k
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EdgeR RNAseq -- best way to deal with random effects
rnaseq edger written 12 months ago by emb13 • 0 • updated 21 days ago by gil.hornung • 0
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How can I run a paired RankProd analysis in R?
rnaseq rankprod R paired written 6 weeks ago by joker33 • 0 • updated 6 weeks ago by James W. MacDonald ♦ 52k
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Defining the design for a complicated multi-level experiment in Limma
rnaseq limma R voom written 6 weeks ago by Colari19 • 0 • updated 6 weeks ago by James W. MacDonald ♦ 52k
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DESeq2: design = ~1 For Normalisation Only.
rnaseq normalization limma deseq2 tcga written 7 weeks ago by Alex Greenshields-Watson • 0 • updated 7 weeks ago by Michael Love ♦ 26k
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Pathviews for DE list of genes
rnaseq pathway analysis pathviews written 7 weeks ago by sofia.lundahl • 0 • updated 7 weeks ago by Michael Love ♦ 26k
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Combining RSEM Files with dif row # for tximport
rnaseq deseq2 tximport written 9 weeks ago by venura • 0 • updated 9 weeks ago by Michael Love ♦ 26k
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Unexpected results while analyzing a subset of genes in GEO RNAseq dataset containing TPM values
rnaseq limma R differential expression tpm written 10 weeks ago by atakanekiz • 30 • updated 10 weeks ago by Steve Lianoglou ♦ 12k
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How to normalize RNA-seq data if majority of transcripts expected to be differentially expressed vs control condition?
rnaseq edger written 10 weeks ago by gdeniz • 0 • updated 10 weeks ago by Gordon Smyth ♦ 39k
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pvaluecutoff meaning in enrichKEGG
rnaseq kegg written 10 weeks ago by sportiellomike • 0
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Variation between technical replicates (DESeq2, batch effects)
rnaseq deseq2 differential expression batch effect replicates written 11 weeks ago by Nik dAK • 10 • updated 11 weeks ago by Michael Love ♦ 26k
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Differential gene expression anlaysis?
rnaseq normalization R written 12 weeks ago by 1234anjalianjali1234 • 0 • updated 12 weeks ago by Gordon Smyth ♦ 39k
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cpm filtering parameter
rnaseq edger transcriptomics cpm filtering metatranscriptomics written 3 months ago by vm.higareda • 0 • updated 3 months ago by Gordon Smyth ♦ 39k
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DESeq2 RNAseq differential expression analysis
rnaseq deseq2 written 3 months ago by adeler001 • 0 • updated 3 months ago by Michael Love ♦ 26k
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DESeq2 unpaired RNAseq analysis
rnaseq deseq2 written 3 months ago by adeler001 • 0 • updated 3 months ago by Michael Love ♦ 26k
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DESeq2: Normalization of allele specific counts in RNA-seq
rnaseq normalization deseq2 allele-specific written 3 months ago by Ankit • 0 • updated 3 months ago by Michael Love ♦ 26k
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Removing Batch effect on the raw counts or normalised counts
rnaseq deseq2 batch effect written 3 months ago by chudar.chudar • 0 • updated 3 months ago by Michael Love ♦ 26k
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RNA-seq normalization without filtering
rnaseq normalization edger deseq2 written 4 months ago by Lin • 50 • updated 4 months ago by Steve Lianoglou ♦ 12k
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