kallisto paper analysis
This repo contains all the analysis to reproduce the results in the kallisto paper.
The latest version of this analysis is accessible via GitHub.
- Install snakemake
- Download software listed in
config.pyand place it in the appropriate directory in
- Download and install
Ralong with dependencies listed below (R dependencies section)
Running the scripts
Everything is run using
Start with the top level script as there are some dependencies.
The data and dependencies should get pulled automatically (assuming software has been appropriately installed).
If you wish to run everything, you can simply run the
run_all.sh script in the top level.
The version of
R we used to generate results is 3.2.3.
First, install Bioconductor:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R")
Then, you should be able to install packages using the
Install these packages using
devtools::install_github('pachterlab/sleuth', ref = 'v0.27.3')
devtools::install_github('pimentel/mamabear', ref = 'v0.1')