Bioconductor SubsetByOverlaps

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InteractionSet subsetByOverlaps GenomicInteractions

21 months ago LaureTomas ▴ 10

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4.6k

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findOverlaps GPos GenomicRanges subsetByOverlaps

updated 3.3 years ago by James W. MacDonald 68k • written 3.3 years ago by Robert ▴ 10

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granges genomicranges iranges subsetByOverlaps

updated 3.2 years ago by b.simpson • 0 • written 9.6 years ago by vinod.acear ▴ 50

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2.4k

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genomicranges subsetbyoverlaps granges findoverlaps

7.6 years ago Assa Yeroslaviz ★ 1.5k

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2.0k

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granges findoverlaps subsetbyoverlaps

updated 9.5 years ago by Michael Lawrence ★ 11k • written 9.5 years ago by vinod.acear ▴ 50

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1.9k

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granges genomicranges findoverlaps subsetbyoverlaps

updated 9.5 years ago by Hervé Pagès 16k • written 9.5 years ago by vinod.acear ▴ 50

6 results • Page 1 of 1

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Comment: Differing results with DESeq2 by JKim • 0

My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …

Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k

Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…

Answer: RNA-seq input to GRaNIE by James W. MacDonald 68k

This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…

Answer: Help using reduceSimMatrix with a custom annotation by sergisayolspuig ▴ 80

Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…

Answer: Analyzing TnSeq data with DESeq2 by cold.wolverine.arku • 0

That's a great use case of DESeq2! Even though it's not specifically tailored for TnSeq data, your approach to normalize and run explorator…

Votes

A: Unbalanced experiment with multiple samples from each patient.

A: Understanding contrasts limma

Answer: ROAST for small sets

A: conceptual question about FDR, FDR adjusted p-value and q-value

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