Bioconductor RamiGO

Showing : RamiGO • reset

votes

replies

1.3k

views

RamiGO R gene ontology igraph

8.9 years ago bkellman • 0

votes

1.1k

views

ramigo annotation readAmigoDot getAmigoTree

9.6 years ago evepash • 0

votes

replies

1.0k

views

ramigo

9.7 years ago Asta Laiho ▴ 120

votes

1.2k

views

GO RamiGO GO RamiGO

updated 10.8 years ago by Dan Tenenbaum ★ 8.2k • written 10.8 years ago by Asta Laiho ▴ 120

votes

replies

1.6k

views

RamiGO RamiGO

updated 10.8 years ago by Dan Tenenbaum ★ 8.2k • written 10.8 years ago by suzy.stiegelmeyer@syngenta.com ▴ 40

votes

replies

1.2k

views

GO RamiGO GO RamiGO

12.5 years ago Guest User ★ 13k

6 results • Page 1 of 1

Recent ...

Replies

Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu by Nicholas • 0

Got it, so using the GTF directly rather than any of the annotation packages will yield more accurate results than any of the packages? I g…

Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu by James W. MacDonald 67k

I agree that it's difficult to match an `EnsDb` object to the build, but I think that is orthogonal to OP's issue, which is mapping transcr…

Comment: Why did PCA plots look exactly the same after adjusting for batch covariate in D by Quang ▴ 10

I see. Thank you for your advice! In my case per James' suggestions, I redesigned the model to `~ DonorID + Subset + Conditions` as Date_…

Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu by ATpoint ★ 4.6k

> that you should stick with whatever IDs you started with, Meaning, you got your fasta file for the kallisto index from somewhere, e.g. …

Comment: Why did PCA plots look exactly the same after adjusting for batch covariate in D by Michael Love 43k

Think of two separate paths in DESeq2: 1) visualization/EDA and 2) testing. For (1) you use vst(), removeBatchEffect(), etc. The design is…

Votes

Answer: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu

Comment: Why did PCA plots look exactly the same after adjusting for batch covariate in D

Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?

A: Trajectory analysis for single cell sequencing

Answer: Annotation with org.Hs.eg.db Genome Build 38

Awards • All

Popular Question to Assa Yeroslaviz ★ 1.5k