Bioconductor Tophat

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votes

963

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snpeff python tophat r RNAseq123

updated 3.3 years ago by Kevin Blighe ★ 4.0k • written 3.3 years ago by kusum • 0

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1.0k

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noiseq rsubread tophat bowtie bowtie2

5.4 years ago Marcelo Laia ▴ 450

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1.1k

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topGO tophat kolmogorov-smirnov test

updated 7.3 years ago by James W. MacDonald 67k • written 7.3 years ago by aaronrosenstein • 0

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replies

2.3k

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R rnaseq tophat summarizeoverlaps systempiper

updated 8.0 years ago by Thomas Girke ★ 1.7k • written 8.0 years ago by abass.conteh • 0

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8.0k

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deseq deseq2 edger tophat bowtie

9.4 years ago ysdel ▴ 40

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2.6k

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rnaseq summarizeOverlaps deseq2 tophat genomicalignments

updated 10.0 years ago by Dan Tenenbaum ★ 8.2k • written 10.0 years ago by alejandro.colaneri ▴ 20

6 results • Page 1 of 1

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Answer: Is it possible to parallelise saveHDF5SummarizedExperiment by Hervé Pagès 16k

Hi Stefano, Unfortunately HDF5 doesn't support concurrent writing so parallelising is not an option. A few things that maybe could help: …

Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db? by James W. MacDonald 67k

It's a simple two-liner in [getsrc.sh][1] ``` awk -F'\t' 'BEGIN {OFS=FS} {if($3 != $11 && $11 != "-") $3 = $11; print $0}' gene_info > tmp…

Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db? by Guido Hooiveld ★ 4.1k

Thanks for changing this! Just to confirm I understood it correctly: the `Symbol` will (still) be used, and will be replaced by `Symbol fro…

Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db? by James W. MacDonald 67k

OK, there are 157 MT genes in maybe 6 species for which the symbols are not correct, and I added code to swap the 'Symbol from nomenclature…

Comment: Tximport with RSEM error by Michael Love 42k

Would you post a new issue with example code and maybe what the files look like?

Votes

Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db?

Answer: Supercells with Basilisk fails for dtype('float64') to dtype('int64') conversion

A: GOseq analysis with only upregulated or downregulated genes

Answer: Properly constructing a hypergeometric test

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