PI wants to create a pipeline app for single cell, help i’m a lowly undergrad.
Hi i’m an undergrad here learning bioinformatics and specifically single cell analysis as part of building a pipeline for my PI. He has no background in it and i’m self teaching myself everything.
Part of the project is he wants to build a UI/app that allows the lab to essentially plugin certain parameters and pump out a graph like UMAP or tsne. Essentially, standardizing it for easy use.
Problem is from what i’ve learned is that the analysis is a bit more complicated than just adjusting a few parameters with a drop down. Now i don’t know much but I believe TSNEs are models that cannot be applied to different data sets because it is non parametric. I brought this up to him and he said that they have set seeds and i can set the seed to be the same.
I kinda know what that means but kinda don’t. I have a vague idea of dimensionality reduction, eigen vectors, etc.
Would making an app/internal pipeline be possible with these kind of things? Wouldn’t it require a person to actually handle the data or code to specify it per data set?