Bioconductor IntegerList

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r iranges findoverlaps IntegerList List

8.4 years ago • updated 8.1 years ago jian_liangli • 0

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r iranges integerlist DataFrame

updated 8.1 years ago by Jurat Shahidin ▴ 80 • written 8.1 years ago by jian_liangli • 0

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r iranges integerlist

8.2 years ago Jurat Shahidin ▴ 80

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r s4vectors integerlist iranges

updated 8.3 years ago by Michael Lawrence ★ 11k • written 8.3 years ago by jian_liangli • 0

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iranges integerlist s4

8.4 years ago Jurat Shahidin ▴ 80

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s4 coercion iranges integerlist

8.4 years ago jian_liangli • 0

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Comment: Identifying potentially associated gene set to drug response using GSVA by coolmathforkids2 • 0

It is always helpful to see clear explanations and solutions for bioconductor related challenges. Posts like this make the community a valu…

Comment: minfi latest update for EPIC V2 chip by macdonaldfrench7286566 • 0

Yes, the most updated analysis for the EPIC V2 chip using the minfi package still involves using the annotations provided by jokergoo. *Th…

Answer: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k

To compute CPM values from edgeR: ``` y <- DGEList(counts = counts, samples = samples, genes = genes, group = samples$Disease_status) y <- …

Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Gordon Smyth 52k

Follow the vignette. It explains how to call edgeR's cpm function to use the offsets.

Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Andre • 0

But if i want to do another type of analysis like Wilcoxon/Mann-Whitney and want to incorporate salmon offset can i simply use the cpm func…

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Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?

Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio

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