Bioconductor Tophat

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1.1k

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snpeff python tophat r RNAseq123

updated 3.8 years ago by Kevin Blighe ★ 4.0k • written 3.8 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 7.9 years ago by James W. MacDonald 68k • written 7.9 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 10.5 years ago by Dan Tenenbaum ★ 8.2k • written 10.5 years ago by alejandro.colaneri ▴ 20

6 results • Page 1 of 1

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Comment: Heatmap of rnaseq data with z-score scale by giovanna • 0

![Figure1][1]![Figure2][2] [1]: /media/images/d62918c5-2886-44ae-930d-91d292c3 [2]: /media/images/421df232-8a9c-4016-bc4a-431ca57a

Comment: parameters of filterByExpr by caroline.zanchi ▴ 10

Ah yes sorry :) But then I still do not understand why is it that on the plot I attached, the gene definitely has non-0 counts in less than…

Answer: Typo in the help of lmFit() by Gordon Smyth 52k

Thanks for the heads-up. > The _Details_ in the documentation of lmFit() still says that the default correlation is 0.75 Yes, you're righ…

Comment: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm by caroline.zanchi ▴ 10

Thank you ! ![enter image description here][1] In the end I did ```r rn2 <- select(org.Dm.eg.db, row.names(cent_expr_matrix), "GENENAME"…

Answer: Memory issue while using "quickcluster" and "computeSumFactors" functions on sin by James W. MacDonald 68k

The obvious solution is to use cloud computing, which is likely cheaper than getting more RAM for your computer.

Votes

Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm

Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)

Comment: Check removeBatchEffect effectiveness

Answer: Check removeBatchEffect effectiveness

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