Bioconductor Parameters

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xcms adjustRtime parameters scantime error biocparallel error

6.1 years ago abrsoule ▴ 30

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1.6k

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MAST AIC calcuation Parameters single cell hurdle model

updated 19 months ago by rproendo ▴ 30 • written 6.7 years ago by mcalgaro93 • 0

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1.6k

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rtracklayer liftOver parameters minMatch

updated 7.6 years ago by Michael Lawrence ★ 11k • written 7.6 years ago by Nik dAK ▴ 10

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1.9k

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Volcano plot Parameters

updated 8.1 years ago by Gordon Smyth 53k • written 8.1 years ago by Sanches • 0

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1.3k

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lpsymphony R parameters control warm start

updated 9.4 years ago by Wolfgang Huber ★ 13k • written 9.4 years ago by chiel • 0

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Comment: deseq2 filter the low counts by Michael Love 43k

Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering

Comment: deseq2 filter the low counts by empty_mt • 0

Hi Michael, My matrix consists of 36 samples from 6 treatments (6 samples/ treatment), whether I adjust prefiltering parameters or not, in…

Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0

That works. I didn't realize what you said about HDF5 files. We always keep those and archive the MTX files. I'm able to read in the file…

Comment: DESeq2 interactions by Michael Love 43k

GPT even v4 gives pretty good answers to DESeq2 questions that are similar to those already posted on the support site. I've also noticed …

Answer: Important: Bioconductor Release 3.22 Delayed by shepherl 4.2k

We will continue with the release on Thursday October 30th. We have shifted one day as originally planned. Thank you

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Answer: DESeq2 interactions

Answer: Important: Bioconductor Release 3.22 Delayed

A: Multi-level experiments in Limma

Answer: Should voomWithQualityWeights still be used when the sample-specific weights var

Answer: DESeq2 for candidate gene analysis

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