Bioconductor Refseq

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1.0k

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refseq Bioconductor conversion

4.1 years ago heiko_kin ▴ 60

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683

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RefSeq Chromosome Mutalyzer

4.7 years ago heiko_kin ▴ 60

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2.4k

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tximport Gene IDs txdb RefSeq Salmon

updated 4.9 years ago by Michael Love 43k • written 4.9 years ago by holmkn • 0

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3.1k

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edgeR ENEMBL RefSeq

updated 5.8 years ago by Gordon Smyth 52k • written 5.8 years ago by mzillur • 0

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2.8k

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genomicfeatures maketxdbfromucsc refseq

updated 8.5 years ago by Hervé Pagès 16k • written 8.5 years ago by Sebastien Vigneau ▴ 10

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4.0k

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ncbi refseq maketxdbfromgff fetchExtendedChromInfoFromUCSC genomeinfodb

updated 9.0 years ago by Hervé Pagès 16k • written 9.0 years ago by gokcen.eraslan ▴ 10

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3.1k

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promoter granges refseq ucsc organismdb

updated 9.1 years ago by Robert Castelo ★ 3.4k • written 9.1 years ago by efoss ▴ 10

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4.0k

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refseq annotationhub

updated 9.3 years ago by Martin Morgan 25k • written 9.3 years ago by dalloliogm ▴ 50

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1.8k

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customprodb dbsnp refseq varianttools

updated 9.5 years ago by xiaojing.wang ▴ 50 • written 9.5 years ago by kristenbeck527 • 0

9 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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