https://github.com/mikelove/bioc-proposal
https://github.com/mikelove/bioc-proposal
Last synced: 3 months ago
JSON representation
- Host: GitHub
- URL: https://github.com/mikelove/bioc-proposal
- Owner: mikelove
- Created: 2018-05-03T19:05:13.000Z (about 7 years ago)
- Default Branch: master
- Last Pushed: 2020-05-29T01:47:04.000Z (about 5 years ago)
- Last Synced: 2025-01-22T07:51:15.258Z (4 months ago)
- Size: 12.7 KB
- Stars: 0
- Watchers: 4
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# Importing alevin scRNA-seq counts into R/Bioconductor
# Instructor(s) name(s) and contact information
- Michael Love (michaelisaiahlove at gmail dot com)
- Avi Srivastava (asrivastava at nygenome dot org)
# Workshop Package:
# Workshop Description
In this workshop, we will demonstrate basics of quantification of
droplet-based scRNA-seq reads using alevin, producing a count matrix
for import into Bioconductor using tximeta, in the end
producing a *SingleCellExperiment* object. We will also demonstrate
the ability of alevin to provide quantification uncertainty on the
count matrix, and visualize this uncertainty across cells.
We plan the workshop to be an instructor-led live demo with time
for questions and interactions with the participants. We imagine that
the target participant for the workshop probably has some dscRNA-seq
data, and knows about e.g. generating a count matrix with *CellRanger*.
We will show an alternative quantification pipeline and explain its
benefits. We will show hand off of the data to OSCA (Bioconductor's
online book) as well as to Seurat.
## Pre-requisites
* Basic knowledge of R syntax
* General understanding of scRNA-seq experiment
## Workshop Participation
Students will participate by following along a live demo, and asking
questions or providing feedback throughout.
## _R_ / _Bioconductor_ packages used
- tximeta
- SingleCellExperiment
- fishpond
- scran
- Seurat
## Time outline
An example for a 45-minute workshop:
| Activity | Time |
|------------------------------|------|
| alevin for droplet scRNA-seq | 20m |
| importing counts into Bioc | 5m |
| examination of counts data | 10m |
| examination of uncertainty | 10m |
# Workshop goals and objectives
## Learning goals
- understand how scRNA-seq quantification methods work and
understanding their limits
- describe how Bioconductor's classes including
*SingleCellExperiment* facilitate reproducibility through
tracking metadata on the samples/cells and the genomic ranges
## Learning objectives
- see code to run alevin, quantifying scRNA-seq reads to make a gene count matrix
- import scRNA-seq count data including genomic ranges
- manipulate a SingleCellExperiment
- examine scRNA-seq counts over cell labels
- examine uncertainty estimates for counts
- hand-off to Seurat workflow
- hand-off to OSCA workflows