Bioconductor Batch correction

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2.0k

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scrna-seq integration batch correction

updated 5.2 years ago by Aaron Lun ★ 28k • written 5.2 years ago by p.joshi ▴ 40

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1.4k

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methylation ComBat Linear models batch correction AIC

updated 5.3 years ago by Kevin Blighe ★ 4.0k • written 5.3 years ago by lucasmiranda42 • 0

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844

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DESeq2 batch correction

updated 5.4 years ago by James W. MacDonald 68k • written 5.4 years ago by MT ▴ 10

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1.2k

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Diffbind ATAC batch correction blocking factor

updated 5.6 years ago by Rory Stark ★ 5.2k • written 5.6 years ago by rm1238 • 0

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1.2k

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deseq2 differential expression batch correction design

updated 5.8 years ago by Michael Love 43k • written 5.8 years ago by wunderl ▴ 40

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1.8k

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deseq2 differential expression batch correction

updated 5.8 years ago by Michael Love 43k • written 5.8 years ago by wunderl ▴ 40

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2.3k

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SC3 Scater Scran scRNA-Seq Batch Correction

updated 6.0 years ago by Vladimir Kiselev ▴ 150 • written 6.0 years ago by hamza_karakurt ▴ 60

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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.

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

Thank you so much for your answer, very useful!

Votes

Answer: Help with the code for "BiocNeighbors::generic_find_knn() function used by scran

Is it possible to speed up VariantAnnotation's rowRanges function when converting to a dataframe?

Answer: Is it possible to speed up VariantAnnotation's rowRanges function when convertin

Comment: ComBat with repeated measures

Answer: Package developing and interoperation with Bioconductor

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