Bioconductor Tophat

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1.1k

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snpeff python tophat r RNAseq123

updated 3.7 years ago by Kevin Blighe ★ 4.0k • written 3.7 years ago by kusum • 0

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1.1k

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noiseq rsubread tophat bowtie bowtie2

5.9 years ago Marcelo Laia ▴ 450

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1.2k

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topGO tophat kolmogorov-smirnov test

updated 7.8 years ago by James W. MacDonald 68k • written 7.8 years ago by aaronrosenstein • 0

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2.5k

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R rnaseq tophat summarizeoverlaps systempiper

updated 8.5 years ago by Thomas Girke ★ 1.7k • written 8.5 years ago by abass.conteh • 0

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8.4k

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deseq deseq2 edger tophat bowtie

9.9 years ago ysdel ▴ 40

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2.7k

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rnaseq summarizeOverlaps deseq2 tophat genomicalignments

updated 10.4 years ago by Dan Tenenbaum ★ 8.2k • written 10.4 years ago by alejandro.colaneri ▴ 20

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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