Bioconductor MSIGDB

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770

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GSEABase fgsea msigdb GeneSetEnrichment

4 months ago Assa Yeroslaviz ★ 1.5k

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342

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msigdb fgsea msig

7 months ago Tanvi • 0

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655

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geneset GeneSetEnrichment msigdb

10 months ago Seongsu • 0

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770

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msigdb gmt GSEA

written 10 months ago by Georg • 0

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2.6k

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ssgsea GSVA biotype proteincoding msigdb

updated 4 months ago by Ginny • 0 • written 14 months ago by snijesh ▴ 200

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1.9k

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msigdb GSEABase GSVA

updated 2.8 years ago by Robert Castelo ★ 3.4k • written 2.8 years ago by forlani.luca • 0

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2.2k

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gseabase msigdb genesetcollection Tutorial

written 6.6 years ago by t.kuilman ▴ 170

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4.8k

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clusterprofiler GSEA MSIGDB

updated 6.9 years ago by Guangchuang Yu ★ 1.2k • written 6.9 years ago by thomasjenner333 • 0

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1.6k

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limma romer msigdb

updated 9.4 years ago by James W. MacDonald 67k • written 9.4 years ago by Jon Manning ▴ 40

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1.5k

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category gostats msigdb hypergeometric test

9.5 years ago petyuk ▴ 70

10 results • Page 1 of 1

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Comment: input for singR function by iamin053 • 0

Hi Paria, I'm wondering if you were able to get an answer on this please. I would greatly appreciate any comments!

Comment: build samplesheet and plot profile by yf • 0

![enter image description here][1] [1]: /media/images/8ea93bd0-bc90-443d-a332-4701f54a

Answer: I am having issues with bowtie2_build by James W. MacDonald 67k

Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…

Answer: DEG analysis across multiple timepoints, treatments and tissues by Michael Love 43k

Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…

Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k

FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…

Votes

A: Doubt about the "zero expression" genes or genes with no reads at all in the co

Answer: Unable to install nloptr

Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?

C: How does edgeR cpm function calculate log(CPM) values?

Answer: Selection of correct coefficients or contrasts in DESeq2

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