Bioconductor Phylogenetics

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phyloseq Phylogenetics

updated 2.1 years ago by yrkkhdesiserials • 0 • written 3.7 years ago by memy • 0

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phyloseq Phylogenetics

updated 2.2 years ago by RMiller ▴ 20 • written 2.2 years ago by kevin • 0

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Phylogenetics genomes R MultipleSequenceAlignment Bioconductor

3.8 years ago • updated 3.7 years ago K. • 0

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Phylogenetics

3.8 years ago Lanjamarina • 0

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igraph networkanalysis Phylogenetics phyloseq

updated 6 weeks ago by solarsunyy • 0 • written 4.4 years ago by Chantel • 0

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rna-seq phylogenetics protein modelling single-cell sequencing Job

4.8 years ago liam.childs • 0

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Comment: Check removeBatchEffect effectiveness by Gordon Smyth 52k

Both of your matrices, `design_batcheffects` and `design_timepoint`, span the intercept term, which will cause a warning about NA coefficie…

Comment: DiffBind - question on the use of filtered or unfiltered input data by sloperun3az • 0

Your essay was beneficial to me, and I found it to be very useful. Thank you for writing it. You give a wealth of knowledge that is not onl…

Comment: compute_fasta_digest does not match Salmon index hash by sloperun3az • 0

The people who are reading your work are not taken into consideration, even though you appear to have a solid understanding of the subject …

Comment: parameters of filterByExpr by Paul Harrison ▴ 110

It might be worth trying limma-voom (or limma-trend) instead of a GLM based method. In our experience these are less prone to this problem.…

Comment: limma::voom vs edgeR::voomLmFit - when to use? by Gordon Smyth 52k

voomLmFit() is in edgeR instead of limma because it needs to call edgeR::glmFit() internally to determine which of the zero observations al…

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Comment: Check removeBatchEffect effectiveness

Answer: Check removeBatchEffect effectiveness

A: what should I do with many zero counts from Salmon quantification

Comment: parameters of filterByExpr

GAlignments Cigar to GRanges

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