Awesome
sleuth paper analysis
This repo contains all of the code to reproduce the results in the sleuth paper.
The repository at https://github.com/pachterlab/sleuth_paper_analysis should always have an updated version that is hopefully bug free.
Preliminaries
- Install snakemake
- Download and install
R
along with dependencies listed below (R dependencies section) - Updated the
BASE
variable inconfig.py
to represent the base path on your system
Organization
The code is organized into a few different directories, each with a theme:
annotation
: pulls down the different annotations used and creates indicesbottomly
: analysis related to the Bottomly et al. data, particular the 'self-consistency FDR' experimentscuffdiff2_analysis
: analysis of the Trapnell et al. dataset to extract effect sizes from that datasetgeuvadis
: the bulk of the simulations, based on results from the GEUVADIS datasimulation_core
: dependencies for the simulations in thegeuvadis
directorysoftware
: the bulk of the software used, not including the R dependencies
R dependencies
Install using install.packages()
from CRAN
cowplot
devtools
dplyr
data.table
ggplot2
jsonlite
reshape2
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
BitSeq
DESeq
DESeq2
EBSeq
edgeR
limma
from GitHub
sleuth v0.28.1
fork with some modifications:devtools::install_github('pachterlab/sleuth', ref = 'nm')
mamabear v0.3
:devtools::install_github('pimentel/mamabear', ref = 'v0.3')
Bug reports
Please make them in GitHub issues.