Amanda Kedaigle

icon indicating a website link http://amandakedaigle.com icon indicating an email [email protected]

icon company Broad Institute icon location United States icon location Computational biologist in biotech. Formerly Levin & Arlotta labs at Broad Institute/Harvard, and @fraenkel-lab at MIT

Results 5 comments of Amanda Kedaigle

getCounts with 10X Cellranger output

As an update, I've tried a couple different ways to get around this (both reading out my bam file as a sam and changing each CB tag to an RG...

Add mRNA nodes & interactions to forest

OK, so I'll add the first part of this to GarNet as well, but basically, the output of Garnet right now is a file with three columns: "Transcription Factor Slope...

Add mRNA nodes & interactions to forest

Thanks! Just so you know, I'll be out of town and starting this after the 19th

Motif matching when using mouse data

Hi David! If you're using RStudio you can write `View(function_name)` to see code for a function in a loaded package (or `View(package_name::function_name)`. I believe that outside of RStudio you can...

Motif matching when using mouse data

I was using Seurat, but was still on v4 - didn't run into that one!