Bioconductor Soft power

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RNA-seq WGCNA package soft power

6.7 years ago modarzi ▴ 10

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Comment: Design Matrix with paired and independent samples plus RUVg Spike-in normalizati by Mei • 0

I have a similar experiment with 7 paired samples (T0 and T1) in each of 4 outcome groups. I am using RUVr combined with limma-voom, so I a…

Comment: Help with the code for "BiocNeighbors::generic_find_knn() function used by scran by Arctic • 0

Many thanks for the link to the C++ code. I will see if I can find someone with C++ experience to help me with the code breakdown from her…

Answer: Help with the code for "BiocNeighbors::generic_find_knn() function used by scran by Aaron Lun ★ 28k

It's calling C++ code, see the relevant function definitions on [GitHub](https://github.com/knncolle/BiocNeighbors/blob/master/src/generics…

Answer: DESeq2 by ATpoint ★ 4.8k

Time courses are often inevitable batches but you should have done the library prep at the same day, just extract RNA per day. If not then …

Comment: Package developing and interoperation with Bioconductor by slizchap • 0

Thank you so much for your answer. This was very useful, I will optimize my functions so they can handle SE objects.

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Comment: ComBat with repeated measures

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