Bioconductor Sushi

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sushi bed

6.6 years ago maltethodberg ▴ 180

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sushi plotGenes

7.3 years ago portia.mcghan • 0

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sushi

8.6 years ago snamjoshi87 ▴ 40

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sushi plotBed data.frame

9.0 years ago waqasnayab • 0

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sushi plotBed

updated 9.1 years ago by dphansti ▴ 10 • written 9.2 years ago by Dimitris Polychronopoulos ▴ 80

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Sushi

updated 9.1 years ago by dphansti ▴ 10 • written 9.1 years ago by Till ▴ 30

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R sushi

updated 9.2 years ago by dphansti ▴ 10 • written 9.3 years ago by javier.mendoza • 0

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sushi

updated 9.6 years ago by Steve Lianoglou ★ 13k • written 9.7 years ago by Bogdan ▴ 670

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Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0

`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/

Comment: error in ChAMP loading file by janwilseo • 0

Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)

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

Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…

Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0

One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…

Comment: DESeq2 Design controlling for gender by donnycrimson • 0

On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…

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DiffBind; Error: No sites have activity greater than filter value

remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline

How to remove X & Y chromosome genes from RNAseq data

Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?

A: Unbalanced experiment with multiple samples from each patient.

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