Bioconductor GAGE package

Showing : GAGE package • reset

votes

replies

1.2k

views

gage package gage

7.3 years ago melkile26 • 0

vote

replies

1.7k

views

gage gage package gene expression matrix gene set analysis

7.3 years ago atakanekiz ▴ 30

votes

replies

3.4k

views

gage package error

updated 7.5 years ago by James W. MacDonald 68k • written 7.5 years ago by Miskey, Csaba ▴ 20

votes

replies

4.5k

views

gage gage package pathview rna-seq

updated 3.7 years ago by Helen • 0 • written 7.7 years ago by tarun2 • 0

votes

replies

2.6k

views

kegg geneset genelist gage package

updated 8.2 years ago by Gordon Smyth 53k • written 8.2 years ago by sup230 ▴ 30

vote

replies

1.8k

views

gage package deseq2

8.3 years ago sup230 ▴ 30

votes

replies

2.1k

views

gage gage package

updated 9.0 years ago by Luo Weijun ★ 1.6k • written 9.1 years ago by Michael • 0

vote

replies

1.9k

views

R gage package rnaseq pathview

9.3 years ago • updated 9.2 years ago joanito.liberti • 0

votes

1.3k

views

gage package path.ids RNA-Seq

9.3 years ago rl1385 • 0

votes

replies

1.2k

views

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

9.4 years ago smt8n • 0

10 results • Page 1 of 1

Recent ...

Replies

Comment: Getting a large intercept with DESeq2 by James W. MacDonald 68k

As a trivial example, consider this: ``` > model.matrix(~Treatment, data.frame(Treatment = factor(rep(1:3, each = 4)))) (Intercept) Tre…

Answer: Getting a large intercept with DESeq2 by James W. MacDonald 68k

The default parameterization in R is a treatment-contrasts parameterization that sets one of your groups as the baseline. So the intercept …

Answer: Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single C by ATpoint ★ 5.0k

There is no "MUST", but pseudobulk aggregation is beneficial to a) enable use of tested and robust methods such as limma (though it could u…

Answer: Post translational modifications and phosphoproteomics in limpa? by Gordon Smyth 53k

Yes, we use limpa for PTMs ourselves. I assume your data is preprocessed so that each row corresponds to a PTM. You replace dpcQuant() with…

Comment: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif by Matthew Thornton ▴ 380

WOW! Thank you so much for the information. I will do this.

Votes

Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif

Using edgeR or DESeq2 to analyze allele-specific expression?

Answer: DESeq2 design for haplotype MPRA

Answer: Failure to download resources (MeSHDb) from AnnotationHub

Awards • All