Bioconductor Chromatin

Showing : chromatin • reset

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hic diffhic chromatin bedpe

updated 6.4 years ago by Aaron Lun ★ 28k • written 6.4 years ago by gryderart • 0

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1.3k

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epigenomics RNA methylation RNA dynamics chromatin computational biology Job

7.0 years ago mattia pelizzola ▴ 200

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diffbind read counting warning message chromatin atac-seq

updated 7.1 years ago by Gord Brown ▴ 670 • written 7.2 years ago by tgjohnst • 0

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5.0k

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ATAC differential binding analysis no replicates DEseq2 chromatin

7.8 years ago BioinfGuru ▴ 70

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2.0k

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Genomic Assays Chromatin Computational Biology Job

10.2 years ago Doe, Aimee ▴ 40

5 results • Page 1 of 1

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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' ```

Answer: DESeq error: counts matrix should be numeric, currently it has mode: character by ATpoint ★ 4.6k

R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…

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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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