jdiez / bus_notebooks_python

BUS python notebooks

This repository contains example python notebooks for parsing and processing BUS format single-cell RNA-seq files. To run the notebooks, make sure you have kallisto >= 0.45 and bustools installed. The source and binaries are available at:

kallisto

bustools

Getting started

We recommend beginners work through this notebook:

10x v2 chemistry - 6k Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells

Complete notebooks

These notebooks can be used to completely process datasets, starting with downloading the raw data all the way to basic QC plots. They are intended as tutorials on the use of the BUS format.

10x v2 chemistry - 100 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells

10x v2 chemistry - 1k Brain Cells from an E18 Mouse

10x v3 chemistry - 1k Brain Cells from an E18 Mouse

Notebooks in progress

These notebooks are still a work in progress and may not have all the code needed to download and process data automatically.

10x v2 chemistry - 1k PBMCs from a Healthy Donor

10x v3 chemistry - 1k PBMCs from a Healthy Donor

dropseq - GSE63472 mouse retina

celseq1 - GSE62270 mouse intestinal cells

inDrops - GSE102827 mouse visual cortex

Seq-Well - GSE92495 HEK/3T3 mixing, PBMCs, and TB-exposed Macrophages

10x_v2_chemistry - 4k Pan T Cells from a Healthy Donor (From BUS to TCC and GC Matrix example)