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999

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universalmotif scanning enrich_motifs PWM

2.9 years ago alexandre.blais ▴ 50

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2.0k

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pwm pfm jaspar motifdb

updated 6.0 years ago by Bioconductor Community 0 • written 6.1 years ago by chrisclarkson100 ▴ 50

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944

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pwm motifs jaspar meme motif analysis

6.1 years ago rbronste ▴ 60

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2.6k

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pwm tfbstools jaspar

updated 7.3 years ago by Ge Tan ▴ 20 • written 7.3 years ago by chrisclarkson100 ▴ 50

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1.4k

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biostrings seqlogo pwm

updated 8.1 years ago by Marcel Ramos 700 • written 8.1 years ago by clausdkuhn • 0

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981

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biostrings pwm

8.3 years ago Stefanie Tauber ▴ 40

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1.6k

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motifdb matchpwm motif pwmenrich pwm

9.1 years ago vinod.acear ▴ 50

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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: 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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