Bioconductor Bigwig

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1.9k

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DESeq2 edgeR bigwig limma

2.2 years ago • updated 23 months ago Bogdan ▴ 670

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2.2k

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bedgraph wiggleplotr bigwig wig

updated 2.3 years ago by complaintguide • 0 • written 2.4 years ago by Bogdan ▴ 670

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1.7k

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bigWig RNASeqData

2.9 years ago bas_work ▴ 30

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2.1k

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software error BigWig import windows

4.8 years ago lsilva.m • 0

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2.2k

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wiggleplotr bigwig coverage ngs

updated 7.2 years ago by kaur.alasoo ▴ 30 • written 7.2 years ago by borgmichael • 0

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3.5k

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bigwig rtracklayer import granges grangeslist

updated 7.4 years ago by Michael Lawrence ★ 11k • written 7.4 years ago by Assa Yeroslaviz ★ 1.5k

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1.3k

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rtracklayer bigwig import

updated 8.1 years ago by Michael Lawrence ★ 11k • written 8.1 years ago by zx8754 ▴ 10

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1.6k

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bigwig rtracklayer export.bw

updated 8.2 years ago by Michael Lawrence ★ 11k • written 8.2 years ago by story.benjamin ▴ 20

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2.6k

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rtracklayer bigwig

updated 8.9 years ago by laurent.lacroix ▴ 30 • written 8.9 years ago by koneill ▴ 30

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1.4k

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rtracklayer BigWig

updated 9.1 years ago by Michael Lawrence ★ 11k • written 9.1 years ago by dborgesrmit • 0

10 results • Page 1 of 1

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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…

Comment: DESeq error: counts matrix should be numeric, currently it has mode: character by Kucsera • 0

After applying your suggestion, the following error pops up: ``` Error in mde(x) : 'list' object cannot be coerced to type 'double' ```

Votes

A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor

A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use

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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