Bioconductor Msigdb

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945

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msigdb GSEABase GSVA

updated 20 months ago by Robert Castelo ★ 3.0k • written 20 months ago by forlani.luca • 0

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1.7k

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gseabase msigdb genesetcollection Tutorial

5.4 years ago t.kuilman 170

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3.6k

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clusterprofiler GSEA MSIGDB

updated 5.7 years ago by Guangchuang Yu ★ 1.2k • written 5.7 years ago by thomasjenner333 • 0

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1.3k

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limma romer msigdb

updated 8.2 years ago by James W. MacDonald 64k • written 8.3 years ago by Jon Manning ▴ 40

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1.2k

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category gostats msigdb hypergeometric test

8.3 years ago petyuk ▴ 70

5 results • Page 1 of 1

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Comment: Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and by Aastha Kapoor • 0

After several attempts the code has worked. I connected to a faster internet connection. set the timeout (1000000) and run the command. I …

Comment: DESeq2 estimateSizeFactors iterate takes too long by Karthik • 0

Hello, I agree with you, and we are in process of working with collaborators, but I wanted to get a general opinion on the data and get a …

Comment: It's possible to use clusterProfiler without an annotationDBI package by Guido Hooiveld ★ 3.8k

Code to show it works: > library(clusterProfiler) > > ## use provided 10 IDs, plus as last one add ID that has a GO annotati…

Comment: It's possible to use clusterProfiler without an annotationDBI package by Guido Hooiveld ★ 3.8k

You are almost there... Yet - pay attention to the error message (`--> No gene can be mapped.... --> Expected input gene ID: GO:0055080, .…

Comment: Problem loading HDF5Array in R 4.3.2 by Sarah • 0

Thanks for the reply! I tried this and it is crashing at `h5createFile("test.h5")` even after reinstalling **Rhdf5lib** and **rhdf5** It …

Votes

Answer: Limma/DESeq2 for unbalanced nested design (paired samples)

Result from GSEA for non-model organism not as expected

Comment: DESeq2 estimateSizeFactors iterate takes too long

Answer: DESeq2 estimateSizeFactors iterate takes too long

Comment: biomaRtl returns multiple GO terms when filtering on a single GO term in ensembl

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Scholar to Mike Smith ★ 6.2k

Scholar to Hervé Pagès 16k