Showing : gage package • reset
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GAGE for non model organism
gage package gage
6.8 years ago melkile26 • 0
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2
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1.5k
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GAGE analysis with the whole or a subset of matrix
gage gage package gene expression matrix gene set analysis
6.8 years ago atakanekiz ▴ 30
5
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7
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3.2k
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Gage package; go.gset() function error: argument "go_id" is missing
gage package error
updated 7.0 years ago by 68k • written 7.0 years ago by ▴ 20
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2
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4.2k
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Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
gage gage package pathview rna-seq
updated 3.2 years ago by • 0 • written 7.2 years ago by • 0
2
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4
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2.4k
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Can't find gene list for KEGG genesets
kegg geneset genelist gage package
updated 7.7 years ago by 52k • written 7.7 years ago by ▴ 30
1
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0
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1.7k
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DESeq2 - GAGE workflow
gage package deseq2
7.8 years ago sup230 ▴ 30
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1.9k
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How to extract essential genes from pathway (essGene) using DEseq2/GAGE workflow?
gage gage package
updated 8.5 years ago by ★ 1.6k • written 8.6 years ago by • 0
1
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2
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Need to convert gene IDs for GAGE pathway analysis of honey bee RNA-seq data
R gage package rnaseq pathview
8.7 years ago joanito.liberti • 0
0
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1.2k
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Question on Gage
gage package path.ids RNA-Seq
8.7 years ago rl1385 • 0
0
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0
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1.1k
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GAGE package statistical tests
t-test GAGE package Kolmogorov-Smirnov test Gene-Set enrichment
8.8 years ago smt8n • 0
10 results • Page 1 of 1
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Comment: How can I correctly use phyloseq with Docker? by James W. MacDonald 68k
You can use [bioc-run][1] to simplify things as well. [1]: https://github.com/Bioconductor/bioc-run/tree/devel
Comment: How can I correctly use phyloseq with Docker? by James W. MacDonald 68k
You show how you modified the container, but not how you are running it, which is the critical part.
Comment: Discrepancies in normalised count data vs unnormalised by AMgroup • 0
Thank you for your reply. > Per sample all counts are scaled by the same size factor so I strongly assume that something was parsed here …
Comment: Discrepancies in normalised count data vs unnormalised by ATpoint ★ 4.8k
Please show examples using `plotCounts()`. Custom spreadsheets harbor the risk of parsing errors along the way which very often explains wh…
Comment: Cannot extract size factor from DESeq2 analysis by s.malik • 0
Dear Mike, using tximeta and following code, is this fine to extract normalized counts after `sizeFactors(dds)` gives NULL? `dds <- DESeq…
Votes
Answer: How to combine two DESeq2 objects (dds) for analysis
How to combine two DESeq2 objects (dds) for analysis
How can I correctly use phyloseq with Docker?
A: DESeq2::sizeFactors() function does not output the sizeFactor table.
Comment: Filtering after DESeq
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