Bioconductor Tophat

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1.3k

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snpeff python tophat r RNAseq123

updated 4.5 years ago by Kevin Blighe ★ 4.0k • written 4.5 years ago by kusum • 0

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1.3k

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noiseq rsubread tophat bowtie bowtie2

6.6 years ago Marcelo Laia ▴ 450

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1.5k

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topGO tophat kolmogorov-smirnov test

updated 8.5 years ago by James W. MacDonald 68k • written 8.5 years ago by aaronrosenstein • 0

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2.8k

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R rnaseq tophat summarizeoverlaps systempiper

updated 9.2 years ago by Thomas Girke ★ 1.7k • written 9.2 years ago by abass.conteh • 0

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9.0k

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deseq deseq2 edger tophat bowtie

10.6 years ago ysdel ▴ 40

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2.9k

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rnaseq summarizeOverlaps deseq2 tophat genomicalignments

updated 11.2 years ago by Dan Tenenbaum ★ 8.2k • written 11.2 years ago by alejandro.colaneri ▴ 20

6 results • Page 1 of 1

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Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0

Cool, glad to hear I wasn't missing some functionality in DESeq2. I don't know that much about the differences between DESeq2 vs edgeR; my …

Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k

Yes, so for one thing, note that Gordon has provided code for doing what you are asking in edgeR, which you can go ahead and use. You aske…

Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0

I don't think DESeq2 has the ability to do multi-contrast comparisons, at least based on what I can understand of the manual; I can pick mu…

Comment: Upcoming Ensembl API and data access changes - new blog post available by Hugo Gruson • 0

Thanks for the update. To be very explicit: what is going to happen to the Biomart service, on which the biomaRt bioconductor package relie…

Comment: Are individual-mouse-based statistics possible in CellChat? by LillianaVolkman99 • 0

thank you very much. https://www.biostars.org/p/9617271/

Votes

A: DESeq2: Is it possible to convert read counts to expression values via TPM and r

A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen

Comment: limpa analysis advice

Answer: When to use edgeR or limma

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