Awesome
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.
Preliminaries
- Install snakemake
- Download software listed in
config.py
and place it in the appropriate directory insoftware
- Download and install
R
along with dependencies listed below (R dependencies section)
Running the scripts
Everything is run using snakemake
.
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.
R dependencies
The version of R
we used to generate results is 3.2.3.
from CRAN
Install using install.packages()
cowplot
devtools
dplyr
data.table
ggplot2
jsonlite
reshape2
rjson
scales
from Bioconductor
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 biocLite()
function.
biomaRt
GEOquery
SRAdb
from GitHub
Install these packages using devtools
(install.packages('devtools')
)
sleuth
v0.27.3:devtools::install_github('pachterlab/sleuth', ref = 'v0.27.3')
mamabear
v0.1:devtools::install_github('pimentel/mamabear', ref = 'v0.1')