Bioconductor Bed files

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chip-seq granges R bed files

updated 7.1 years ago by spotifywebplayer • 0 • written 7.1 years ago by jinseok • 0

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parclip bedtools bed files gff3

7.6 years ago linuxborg2 • 0

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bed files bedtools filtering chipseq

updated 7.7 years ago by Aaron Lun ★ 29k • written 7.7 years ago by rbronste ▴ 60

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cn.mops bed files getReadCountsFromBAM

8.2 years ago Pau Marc Muñoz Torres ▴ 20

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bed files wavelet rna-seq

updated 8.4 years ago by shepherl 4.2k • written 8.4 years ago by whgsnp • 0

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gene density bed files gff

9.1 years ago birdguy.saikat • 0

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rtracklayer import bed files

9.4 years ago jmr • 0

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fusion bed files gene fusion bed file

9.5 years ago ramaniak • 0

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Comment: Heatmap of the Count Matrix by ArnulfoByrd • 0

Perhaps PCA loadings offer a more comprehensive perspective. Now, thinking back, I recall struggling with a similar data reduction dilemma …

Answer: readBam vs read_bam_insert_metrics by James W. MacDonald 68k

Depends on what you mean by input. If you mean to ask if you use `readBam` to generate something to use as an argument to `read_bam_insert_…

Answer: How to construct a BSgenome object from a custom genome assembly using BSgenomeF by James W. MacDonald 68k

There is an example in the help page for `forgeBSgenomePkgFromTwobitFile`. Have you tried emulating that?

Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k

What you describe sounds a good approach to me. I would also use sample weights (`sample.weights=TRUE` when running `voomLmFit`) and robust…

Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k

I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…

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Answer: Limpa Pipeline Order

A: How barcode-plot enrichment is calculated?

Answer: ROAST compare results with complex design

How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?

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