Software

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

WASP2

WASP2 (under development) is the next generation of the WASP software for allele specific analysis. It currently provides filtering of reads with biased mapping, counting of allele-specific reads, and statistical tests for allelic imbalance. The interface has been greatly simplified and it is more computationaly efficient than WASP. WASP2 is written by Aaron Ho.

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.

Paper GitHub

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

GLiMMIRS

GLiMMIRS is a generalized linear model framework for identifying interactions between enhancers using single-cell CRISPR perturbation data. GLiMMIRS was written by Jessica Zhou and Karthik Guruvayurappan.

Preprint GitHub