Bioconductor Library complexity

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ATACseqQC ATAC-Seq Library complexity estimateLibComplexity

6.1 years ago Gary ▴ 20

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ATACseqQC ATAC-Seq quality analysis fragment size distribution library complexity

updated 6.2 years ago by Julie Zhu ★ 4.3k • written 6.2 years ago by Gary ▴ 20

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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…

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A: Understanding contrasts limma

Answer: ROAST for small sets

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