daylabprojects/daylab_rat_vta_snrna repository overview

Overview

An image made to reproduce the Day lab VTA analysis with minimum dependencies to re-run the code and a number of additional Seurat dependencies which were not used in the analysis (e.g.: DESeq2, multtest, metap which are needed for specific differential expression parameters or functions such as FindConservedMarkers ) but can aid in the utilization of the container for exploratory purposes.

Parent image from Bioconductor release 11. The image tag corresponds to the Seurat version utilized (be sure to indicate a tagname, currently only 3.2.2 for Seurat v3.2.2). Additional package versions can be inspected from containers with sessionInfo()

Code for analysis: https://github.com/Jeremy-Day-Lab/Rat-VTA-snRNA-seq⁠

Quickstart

This container can be started in a similar manner to rocker/rstudio containers. Thus an example:

docker run -d --rm -p 8787:8787 -e PASSWORD=your_pass daylabprojects/daylab_rat_vta_snrna:3.2.2

Optionally add -v `pwd`:/home/rstudio/ to mount your current working directory (e.g.: containing VTA Seurat object) to the container

Go to http://localhost:8787/⁠ and add rstudio username and your password from -e PASSWORD

For questions about this image, please contact Dr. Lara Ianov at [email protected]⁠