Bioconductor MotifbreakR

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Biostrings aminoacid motifbreakR

written 4 months ago by wilson_ava • 0

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1.2k

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GenomeInfoDb motifbreakR

3.7 years ago Chris Seidel ▴ 80

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1.1k

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MotifbreakR R motifs

5.7 years ago camerond • 0

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motifbreakR vcf snps motif analysis

updated 6.5 years ago by Valerie Obenchain ★ 6.8k • written 6.5 years ago by svlachavas ▴ 840

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bioconductor motifbreakr plotmb

7.1 years ago priyankaraina10 • 0

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1.4k

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motifbreakR variantannotation

updated 9.2 years ago by Simon Coetzee ▴ 50 • written 9.2 years ago by ashley.doane ▴ 20

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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' ```

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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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