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BAM files to Genomic Ranges object
Alignment convert Repitools Alignment convert Repitools
updated 5 months ago by • 0 • written 11.3 years ago by ▴ 280
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1.8k
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How to handle multi-TSS genes in Repitools?
repitools promoter tss annotation
6.1 years ago Ryan C. Thompson ★ 7.9k
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2
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cpgDensityCalc function in Repitools giving contradictory tools
repitools bioconductor cpgDensityCalc
7.1 years ago divyswar01 • 0
0
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891
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Analysis of MBD-seq data without ssl control using BayMeth
Baymeth methylation MBD-seq Repitools
7.9 years ago pm2015 • 0
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885
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SssI free analysis in BayMeth/Repitools
repitools
8.8 years ago Matthias Lienhard ▴ 240
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991
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Repitools - featureScores - mappability Bsgenome object
BSgenome BSgenome Repitools BSgenome BSgenome Repitools
10.2 years ago Dario Strbenac ★ 1.5k
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Repitools - featureScores - mappability Bsgenome object
BSgenome BSgenome Repitools BSgenome BSgenome Repitools
10.2 years ago Jaritz,Markus ▴ 20
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5
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Graph of methylation data around TSS - Repitools or other package?
GO Repitools GO Repitools
updated 10.5 years ago by ★ 1.5k • written 10.5 years ago by ★ 1.1k
0
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973
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Analysing grouped datasets in repitools
limma Repitools limma Repitools
11.2 years ago Guest User ★ 13k
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3
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Repitools/ClusterPlots
BSgenome BSgenome Repitools BSgenome BSgenome Repitools
updated 12.5 years ago by ▴ 580 • written 12.5 years ago by ★ 13k
10 results • Page 1 of 1
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Comment: Help with running egsea() by Chris • 0
I tried egsea.ma and got this error: gsa = egsea.ma(fit2, vector_group, probe_annotation, contrasts = contrast_matrix, gs.annots = gs.…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by angelathuynh5 • 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Method to find pathways different between 2 groups by Gordon Smyth 50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Votes
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
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