Bioconductor Bowtie

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noiseq rsubread tophat bowtie bowtie2

5.5 years ago Marcelo Laia ▴ 450

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Bowtie quasr rnaseq

updated 8.8 years ago by Dario Strbenac ★ 1.5k • written 8.8 years ago by tarek.mohamed ▴ 10

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deseq deseq2 edger tophat bowtie

9.4 years ago ysdel ▴ 40

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r bowtie

updated 9.5 years ago by Sean Davis 21k • written 9.5 years ago by a.afshinfard ▴ 10

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Comment: Struggle with the replicates of epic array data by Melisa Tecik • 0

Thanks you so much for the instructions. I also tried M values as you suggested but sadly the result was the same. Apparently, the problem …

Answer: bioconductor packages on bioconda by James W. MacDonald 67k

The bioconda people are responsible for bioconda, so you should ask them if/when they are going to update.

Answer: txdb.mmusculus.ucsc.mm10.knowngene issue on X chromosome by James W. MacDonald 67k

The default for `plotKaryotype` is to use hg19.

Comment: Is it possible to parallelise saveHDF5SummarizedExperiment by Stefano Mangiola ▴ 20

saveTileDBSummarizedExperiment would be awesome. I think we need performance for execution time and memory required to save.

Comment: Create Illmina bead summary data by Liu • 0

Hi! Yes, thank you! I completely agree. I am just curious about how these two files are processed with AVG_Gre and detection p-value. I am …

Votes

Answer: Struggle with the replicates of epic array data

Answer: bioconductor packages on bioconda

Appropriate use of the function treat of the limma package

Comment: Is it recommended to analyze different tissues together when using edgeR

Answer: Deseq2 res Function

Awards • All

Scholar to James W. MacDonald 67k