search

kimpenn / PIVOT

Platform for Interactive analysis and Visualization Of Transcriptomics data
27 stars 16 forks source link

deprecated 10x Rkit package #11

Closed victorlin45 closed 5 years ago

victorlin45 commented 5 years ago

10x no longer offers their Rkit package. Is there still a way for me to get PIVOT to read .cloupe files? Thanks!

eturkes commented 5 years ago

That's right and 10x doesn't seem to distribute older versions. I did some searching around and I came across this: https://github.com/hb-gitified/cellrangerRkit

Try installing it from there and then loading your .cloupe file. Let us know if you have success. I'll try adding it to my Docker container later, let you know when that's ready to go.

Longer term, the dependency should be pretty simply replaced with something like Seurat. So the issue can be closed when that's done.

victorlin45 commented 5 years ago

Thanks for you quick reply! I'll give the link a try and see how that works. Regarding Seurat, I know you guys have added some Seurat outputs in Pivot already. You guys are in the process of incorporate even more/all Seurat features ?

qinzhu commented 5 years ago

For single cell data with large number of cells, I recommend using my recent package VisCello (https://github.com/qinzhu/VisCello.base) for interactive analysis & visualization. This package has several optimizations for large-scale single cell data and has similar features as Seurat. See https://cello.shinyapps.io/celegans/ for example.

qinzhu commented 5 years ago

I think the suggestion by @eturkes should fix the input problem for PIVOT. But this will only work for output by cellranger 2.x, as recent 3.x version used a completely new data structure. I'm little bit tied up this month but can take a look maybe next month. Still, for very large cell number (say >10k), I recommend using VisCello.base.

eturkes commented 5 years ago

@qinzhu oh that's cool, didn't know you had a Seurat alternative!

qinzhu commented 5 years ago

If you have trouble installing the cellrangerRkit you can just copy paste the source code in https://github.com/hb-gitified/cellrangerRkit/blob/master/scripts/rkit-install-2.0.0.R.