Bioconductor Gage package

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gage package gage

6.4 years ago melkile26 • 0

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gage gage package gene expression matrix gene set analysis

6.5 years ago atakanekiz ▴ 30

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3.0k

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gage package error

updated 6.6 years ago by James W. MacDonald 67k • written 6.6 years ago by Miskey, Csaba ▴ 20

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gage gage package pathview rna-seq

updated 2.8 years ago by Helen • 0 • written 6.9 years ago by tarun2 • 0

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2.2k

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kegg geneset genelist gage package

updated 7.4 years ago by Gordon Smyth 52k • written 7.4 years ago by sup230 ▴ 30

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1.6k

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gage package deseq2

7.4 years ago sup230 ▴ 30

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1.8k

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gage gage package

updated 8.2 years ago by Luo Weijun ★ 1.6k • written 8.2 years ago by Michael • 0

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1.6k

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R gage package rnaseq pathview

8.4 years ago joanito.liberti • 0

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1.1k

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gage package path.ids RNA-Seq

8.4 years ago rl1385 • 0

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1.1k

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t-test GAGE package Kolmogorov-Smirnov test Gene-Set enrichment

8.5 years ago smt8n • 0

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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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