Bioconductor Matrixeqtl

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matrixeqtl sva

updated 9 months ago by James W. MacDonald 66k • written 9 months ago by Shila • 0

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MatrixEQTL

updated 2.4 years ago by Michael Love 42k • written 2.4 years ago by Neha • 0

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hg19 liftover matrixeqtl DMRcate

updated 5.1 years ago by James W. MacDonald 66k • written 5.1 years ago by yoursbassanio ▴ 10

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Comment: Trouble reading samplesheet in with diffbind to create dba by Mallory • 0

Thank you for your reply! There mustve been something wierd going on with my peak formats as you pointed out. I recalled all the peaks and …

Answer: Trouble reading samplesheet in with diffbind to create dba by Anthony • 0

I was struggling with this today too. For me it happened because my peak files were not in the correct format. The "10 elements" refers to …

Comment: gds in GEOmetadb 2023-06-26 version is empty by Frederico Moraes Ferreira ▴ 100

Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz

Comment: Most enriched pathway is not expressed when modifying universe parameter by James W. MacDonald 66k

The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …

Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat by Michael Love 42k

You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.

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Answer: How to do DESeq2 on Kallisto Data

Time-course, comparison of two groups

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