Bioconductor Copy number

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cn.MOPS CNV copy number

5.0 years ago liorglic ▴ 10

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1.7k

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copy number

7.6 years ago mms140130 • 0

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910

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cghcall r cgh copy number

7.8 years ago kitcurtius • 0

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1.5k

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bioconductor ChAMP copy number batch effect normalization

updated 7.9 years ago by rasmus.rydbirk ▴ 10 • written 8.0 years ago by apmishra • 0

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1.2k

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ChAMP champ copy number

8.1 years ago apmishra • 0

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2.9k

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CopywriteR copy number

updated 9.0 years ago by t.kuilman ▴ 170 • written 9.0 years ago by smcnulty • 0

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1.1k

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crlmm copy number

9.9 years ago kforner • 0

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Answer: SingleR with multiple single cell references by Aaron Lun ★ 28k

> Is it necessary to piece together the individual steps manually (e.g. aggregateReference, trainSingleR, classifySingleR, combineRecompute…

Answer: Automatically install dependencies by ATpoint ★ 4.7k

The BiocManager, which is sort of an extended wrapper around `install.packages`, installs all R dependencies. If you see errors then this i…

Answer: To count or not to count multi-overlapping reads? by Gordon Smyth 52k

> How does it handle reads that map to a gene that is located in a region that also has another gene but on the alternate strand? Overlapp…

Comment: Weird p-values using DESeq2? by ATpoint ★ 4.7k

This does not look like normalized counts but raw counts. Consider using `counts(dds, normalized = TRUE)` or the output of `normTransform()…

Answer: Weird p-values using DESeq2? by Wolfgang Huber ★ 13k

Dear Ingrid, thank you for asking. Can you provide the input count matrix (you can "pseudonymize" the biological conditions and the gene n…

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A: Fraction count for multi mapping reads; how to generate input file for Deseq2 fo

Comment: Weird p-values using DESeq2?

Comment: Overcoming confounding in batch effect correction

Answer: Store Matrix in DataFrame Cell

Answer: enrichGOgradient color change

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