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MaayanLab / enrichr_issues

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Documentation does not describe how bed file is converted to gene #9

Closed malcook closed 3 years ago

malcook commented 3 years ago

presumably is is some version of closest promoter - but it is not made clear AFAICS

BED file input capability - September 9th, 2014 Enrichr can now accept BED files as input for enrichment. Enrichr automatically converts the BED file into a gene list. The species supported are human and mouse. The maximum number of genes to produce from the bed file can be adjusted. If the gene list produced by the conversion has more genes than the maximum, Enrichr will take the best matching 500, 1000 or 2000 genes. The file must have the extension ".bed" and must be uploaded, not copy and pasted.

malcook commented 3 years ago

I found the best answer: A Java module in Enrichr maps the chromosome coordinates listed in input BED files to their nearest coding mouse or human genes - probably should be mentioned on the web site