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Limma residuals matrix
limma written 2 days ago by agustin.gonvi • 10 • updated 1 day ago by Gordon Smyth ♦ 38k
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How to apply a linear mixed model onto an RNA-Seq data?
limma voom rna-seq linear mixed model written 2 days ago by Assa Yeroslaviz • 1.4k
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analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma edger deseq2 combat scrnaseq written 15 days ago by Bogdan • 560 • updated 4 days ago by Andrew_McDavid • 190
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How to create two columns for model matrix used in limma?
limma edger written 6 days ago by Ahdee • 40 • updated 5 days ago by Gordon Smyth ♦ 38k
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News: Course in Berlin- Genomics with R and Bioconductor - September 16-20
limma edger deseq2 news written 10 days ago by info • 0
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Most (90%) DE genes of a contrast were upregulated: implication on the assumptions of TMM-normalisation?
normalization limma edger written 13 days ago by mikhael.manurung • 130 • updated 13 days ago by Gordon Smyth ♦ 38k
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lmFit very slow if there are missing values
limma written 14 days ago by Frederik Ziebell • 0 • updated 13 days ago by Gordon Smyth ♦ 38k
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Limma Design matrix for time series+treatment+batch effect
microarray limma design matrix factorial written 21 days ago by senthil.duraikannukailasam • 0 • updated 17 days ago by Aaron Lun • 24k
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Testing random effects in limma
limma written 23 days ago by c.taylor • 0
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Two-way interaction, linear redundancy
limma caret lme4 lmer lm written 27 days ago by Sindre • 100 • updated 26 days ago by Aaron Lun • 24k
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using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma edger scran scater simplesinglecell written 27 days ago by Bogdan • 560 • updated 26 days ago by Aaron Lun • 24k
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normalization of RNA-seq data after over-expressing the transcription factors
limma edger deseq2 voom written 26 days ago by Bogdan • 560 • updated 26 days ago by Aaron Lun • 24k
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Limma linear fit residual standard deviation calculation
limma written 26 days ago by krassowski.michal • 0 • updated 26 days ago by Gordon Smyth ♦ 38k
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correcting the batch effects in Limma and SVA
limma sva combat written 27 days ago by Bogdan • 560 • updated 27 days ago by Gordon Smyth ♦ 38k
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RNA-Seq normalization for co-expression analysis
limma edger wgcna written 5 weeks ago by Lin • 40 • updated 5 weeks ago by Gordon Smyth ♦ 38k
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Limma for cell components effect on response
limma minfi 450k epic cell components written 5 weeks ago by antgomo • 0 • updated 5 weeks ago by Aaron Lun • 24k
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EdgeR - Model matrix for complex model similar to user guide 3.5 example - but more complex
limma edger written 5 weeks ago by DonnyB • 0 • updated 5 weeks ago by James W. MacDonald ♦ 50k
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Finding genes in a gene set detected by ROAST (or FRY) in limma
limma roast fry written 5 weeks ago by kentfung • 0 • updated 5 weeks ago by Gordon Smyth ♦ 38k
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Difference of difference, paired design
limma edger deseq2 written 5 weeks ago by Bloodgas • 0 • updated 5 weeks ago by swbarnes2 • 240
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Including sva results in SeqGSEA with data with batch effect
limma deseq sva deseq2 seqgsea written 5 weeks ago by kentfung • 0
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Creating contrasts which do not include the reference level in limma, edgeR or DESeq2
limma edger deseq2 written 5 weeks ago by Ben • 0 • updated 5 weeks ago by James W. MacDonald ♦ 50k
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Model matrix for longitudinal pairwise rna-seq data: linear regression or linear mixed model?
limma model matrix linear regression written 6 weeks ago by agm • 0
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Complex multifactorial design with random effects in Limma/voom
limma edger written 6 weeks ago by joasmile84 • 10 • updated 6 weeks ago by Aaron Lun • 24k
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Question regarding model matrix in limma.
limma deseq2 written 6 weeks ago by Ben • 0 • updated 6 weeks ago by James W. MacDonald ♦ 50k
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Blocking factor in limma/voom vs. variancePartition/dream analysis.
limma voom variancepartition dream written 6 weeks ago by Ben • 0 • updated 6 weeks ago by gabriel.hoffman • 30
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