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 in config.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 indices
• bottomly: analysis related to the Bottomly et al. data, particular the 'self-consistency FDR' experiments
• cuffdiff2_analysis: analysis of the Trapnell et al. dataset to extract effect sizes from that dataset
• geuvadis: the bulk of the simulations, based on results from the GEUVADIS data
• simulation_core: dependencies for the simulations in the geuvadis directory
• software: 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.