Software Developed By Group Members:
Written by Jie “Chris” Zheng and hosted on the Broad Institute server, LDHub computes genetic correlations against potentially thousands of other traits and diseases. LD Hub is described here: Zheng J, Erzurumluoglu AM, Elsworth BL, Kemp JP, Howe L, Haycock PC, Hemani G, Tansey K, Laurin C; Early Genetics and Lifecourse Epidemiology (EAGLE) Eczema Consortium, Pourcain BS, Warrington NM, Finucane HK, Price AL, Bulik-Sullivan BK, Anttila V, Paternoster L, Gaunt TR, Evans DM*, Neale BM* (2016). LD Hub: a centralized database and web interface to perform LD score regression that maximizes the potential of summary level GWAS data for SNP heritability and genetic correlation analysis. Bioinformatics, 33(2), 272-279.
Complex Traits Genetics Virtual Lab: https://genoma.io
Written by Gabriel Cuellar Partida with assistance from Mischa Lundberg, Shannon Durso and Daniel Hwang, CTG-VL performs a comprehensive range of post GWAS bioinformatics analyses. CTG-VL is described here: https://www.biorxiv.org/content/10.1101/518027v1
Maternal and Offspring Genetic Effects Power Calculator:
Written by Gunn-Helen Moen- this web calculator estimates the power to detect maternal and or fetal genetic effects on offspring phenotypes. MGPC is described here: Moen GH, Hemani G, Warrington NM, Evans DM (2019). Calculating Power to Detect Maternal and Offspring Genetic Effects in Genetic Association Studies. Behav Genet. 49(3), 327-339. doi: 10.1007/s10519-018-9944-9.
Maternal GCTA: https://github.com/uqzqiao/M-GCTA
Written by Zhen Qiao, M-GCTA estimates the proportion of offspring phenotypic variance explained by maternal (or paternal) genetic effects. The software is described here: Qiao Z, Zheng J, Helgeland Ø, Vaudel M, Johansson S, Njølstad PR, Smith GD, Warrington NM, Evans DM (2019), Introducing M-GCTA a software package to estimate maternal (or paternal) genetic effects on offspring phenotypes. Behav Genet. doi: 10.1007/s10519-019-09969-4.
IMPISH (Imputing Maternal and Paternal Genotypes In Siblings and Half siblings)
Coming soon. Written by Justin Luong, IMPISH enables genotype imputation of parental genotypes for sibling and half sibling pairs, and performs efficient genome-wide conditional association analysis of maternal, paternal and offspring genetic effects in a mixed model framework.