Bioconductor MSIGDB

Showing : MSIGDB • reset

votes

replies

153

views

geneset GeneSetEnrichment msigdb

18 days ago • updated 17 days ago Seongsu • 0

votes

replies

202

views

msigdb gmt GSEA

written 4 weeks ago by Georg • 0

vote

564

views

ssgsea GSVA biotype proteincoding msigdb

updated 4 months ago by Robert Castelo ★ 3.2k • written 4 months ago by snijesh ▴ 20

vote

1.2k

views

msigdb GSEABase GSVA

updated 2.1 years ago by Robert Castelo ★ 3.2k • written 2.1 years ago by forlani.luca • 0

vote

1.9k

views

gseabase msigdb genesetcollection Tutorial

written 5.8 years ago by t.kuilman ▴ 170

votes

replies

4.0k

views

clusterprofiler GSEA MSIGDB

updated 6.1 years ago by Guangchuang Yu ★ 1.2k • written 6.1 years ago by thomasjenner333 • 0

vote

replies

1.4k

views

limma romer msigdb

updated 8.6 years ago by James W. MacDonald 65k • written 8.7 years ago by Jon Manning ▴ 40

votes

replies

1.3k

views

category gostats msigdb hypergeometric test

8.7 years ago petyuk ▴ 70

8 results • Page 1 of 1

Recent ...

Replies

Comment: Which input file is used for DGEList in EgdeR? by i.atanasoai • 0

Understood, Thank you very much for the reply, very kind.

Comment: Which input file is used for DGEList in EgdeR? by Michael Love 41k

"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…

Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Michael Love 41k

These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…

Comment: DEG with low counts by Michael Love 41k

These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…

Comment: DESeq filtering specific to contrasts by Michael Love 41k

If the counts are too low it in one group then you can't make the comparison either way (whether they are filtered out or just under-powere…

Votes

Install/Switch between multiple versions of R, Rstudio, and Bioconductor

A: Docker container with bioconductor and devtools

Answer: OrgDb for maize

Comment: significant difference of p-values with dream() after updating VariancePartition

How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output

Awards • All