Software

bkgd

bkgd is a program for calculating B values across the genome. A B value is an estimate of the effect of background selection at a given site in the genome, given the recombination rate and density of sites under purifying selection.

Paper GitHub

WASP

WASP is a software package for unbiased allele-specific read mapping and molecular QTL discovery written by Bryce van de Geijn and Graham McVicker.

Paper GitHub

RELICS

RELICS is a tool for the discovery of functional sequences from tiling CRISPR screens. RELICS was written by Patrick Fiaux.

Paper GitHub

CRSsim

CRSsim is a tool simulating data generated by CRISPR regulatory screens and assessing the performance of various analysis methods for analyzing CRISPR regulatory screens. CRSsim was written by Patrick Fiaux.

Paper GitHub

VarCA

VarCA is an ensembl method for the discovery of single nucleotide variants and indels from ATAC-seq reads. VarCA was written by Arya Massarat, based on some initial ideas developed in the BreakCA tool developed by Arko Sen.

GitHub

as_analysis

as_analysis is a pipeline for allele-specific expression analysis, which uses WASP to correct for mapping bias but offers a greatly simplified workflow compared to WASP's combined haplotype test (CHT). as_analysis is recommended for users who wish to count allele specific reads, but who do not need to perform QTL mapping using the CHT. This pipeline was written by Arya Massarat.

GitHub