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question on the p value for VIPER results by dorothea
RNAseq VIPER Doth
4 months ago snowmattin • 0
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297
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Using VIPER to compare protein activity in normal vs diseased samples
viper
13 months ago tjbencomo • 0
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1.8k
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Data input for aracne2regulon function in viper package
viper
updated 4 months ago by • 0 • written 3.4 years ago by ▴ 20
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2
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Trying to download VIPER
software error viper
updated 3.3 years ago by 13k • written 3.3 years ago by • 0
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925
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VIPER (Protein Activity Inference) gene expression signature format
VIPER aracne.networks
5.9 years ago user31888 ▴ 30
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Use of Viper with a regulatory network built with my dataset or another one?
viper aracne regulatory network aracne.networks
6.3 years ago ldetorrente ▴ 10
6 results • Page 1 of 1
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Answer: msPurity::spectralMatching Error in getSmeta(con, pids) : No meta data for spect by thomas.nigel.lawson • 0
This has been resolved (Windows Firewall issue) - see github issue https://github.com/computational-metabolomics/msPurity/issues/100
Answer: DESeq2 parameter infernce by Michael Love 39k
We use IRLS which is related to Newton-Raphson method. I suppose you can use any optimization method you prefer. We also sometimes use L-BF…
Answer: DESeq2 with 2 continuous factors, LRT, coeficients and slope by Michael Love 39k
See `?results` which describes what the LFC is when you perform an LRT: "*For analyses using the likelihood ratio test*..." Also in the …
Answer: DESeq2 with sample effect, unequal sample sizes by Michael Love 39k
For statistical analysis plans such as design and coefficient interpretation, I recommend collaborating with a local statistician or someon…
Comment: Bioconductor tool for curating annotations? by Lluís Revilla Sancho ▴ 700
I think you can find those transcripts not overlapping with a GRanges object easily via ?GenomicRanges::setdiff, but I don't know how to an…
Votes
Answer: AnnotationForge::makeOrgPackage "argument is missing, with no default" Errors
Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
Answer: Limma-voom with inverse probability weights
A: Limma-voom with external observation weights
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