Bioconductor Locatevariants

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MetID TxDB.Hsapiens.UCSC.hg38.knownGene locateVariants GenomicFeatures VariantAnnotation

21 months ago davidhillis • 0

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genomiclocation canonicaltranscripts locateVariants

updated 3.3 years ago by James W. MacDonald 67k • written 3.3 years ago by Paola • 0

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variantannotation locatevariants metadata mcols

updated 7.0 years ago by Valerie Obenchain ★ 6.8k • written 7.0 years ago by enricoferrero ▴ 660

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variantannotation predict coding locateVariants granges

7.2 years ago tony j • 0

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locatevariants txdb.hsapiens.ucsc.hg19.knowngene variantannotation

7.4 years ago Aleksandra • 0

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txdb.hsapiens.ucsc.hg19.knowngene ucsc annotation locatevariants variantannotation

updated 7.5 years ago by Valerie Obenchain ★ 6.8k • written 7.5 years ago by Lna • 0

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locatevariants variantannotation genomicfeatures

updated 8.1 years ago by Michael Lawrence ★ 11k • written 8.1 years ago by Lna • 0

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2.4k

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variantannotation locatevariants

9.3 years ago Jakob Goldmann • 0

8 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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