scrattch.mapping

Generalized mapping scripts for RNA-seq, Patch-seq or any gene expression data. Assumes that you have built an Allen Institute Taxonomy (AIT) object with scrattch.taxonomy.

Documentation

You can find a detail description of all scrattch.mapping functions here:

Update notes are here:

Docker

We have setup a docker environemnt for scrattch.taxonomy and scrattch.mapping that contains all the required dependencies and the current version of both scrattch.taxonomy and scrattch.mapping. This docker is accessible through docker hub via: njjai/scrattch_mapping:0.6.3.

HPC usage:

Non-interactive

singularity shell --cleanenv docker://njjai/scrattch_mapping:0.6.3 Rscript YOUR_CODE.R

Interactive

singularity shell --cleanenv docker://njjai/scrattch_mapping:0.6.3

Installation

While we advice using the provided docker, you can also install scrattch.mapping directly from github as follows:

Note: slight edits to installation will be needed while repo is private. Also note that doMC may need to be installed manually from the download at https://r-forge.r-project.org/R/?group_id=947 if you use Windows.

# Quickly, but without the vignettes:
devtools::install_github("AllenInstitute/scrattch-mapping")

# More slowly, but with the vignettes:
devtools::install_github("AllenInstitute/scrattch-mapping",build_vignettes=TRUE, force=TRUE)

Note that this strategy might not work outside the docker due to complicated dependencies. Vignettes are provided below.

Usage examples

1. Run Flat, Tree, and Seurat taxonomy mapping This examples shows how to use scrattch.mapping for standard taxonomy mapping.
2. Mapping to HMBA Basal Ganglia AIT This tutorial shows how to map against the HMBA Human and Macaque Basal Ganglia consensus taxonomies.

Reporting issues

If you run into any issues, please let Nelson and Jeremy know or create a new issue in the 'Issues' tab above.