#Software categories in east software#

(October 2019) The PolyLoc software can be downloaded here.

PolyPred is a method that leverages fine-mapping via PolyFun to improve polygenic prediction accuracy, particularly in diverse populations, as described in our manuscript “Leveraging fine-mapping and non-European training data to improve trans-ethnic polygenic risk scores” ( Weissbrod*,Kanai*,Shi* et al.

PolyFun is a method that leverages genome-wide functional annotations to improve fine-mapping power, as described in our manuscript “Functionally-informed fine-mapping and polygenic localization of complex trait heritability” ( Weissbrod et al. (January 2021) The PolyFun software, implementing PolyFun and PolyPred, can be downloaded here. PRS-FH is a method for leveraging family history information to increase polygenic risk score prediction accuracy, as described in our manuscript “Incorporating family history of disease improves polygenic risk scores in diverse populations” ( Hujoel et al. (April 2021) The PRS-FH software can be downloaded here. Postprocessed scRNA-seq data, gene programs, and enhancer-gene linking annotations can be downloaded here. Software for constructing cell type, disease progression and cellular process gene programs can be downloaded here and here. (May 2021) Sc-linker is a framework for integrating scRNA-seq, epigenetic maps and GWAS summary statistics to infer the underlying cell types and processes by which genetic variants influence disease, as described in our manuscript “Identifying disease-critical cell types and cellular processes across the human body by integration of single-cell profiles and human genetics” ( Jagadeesh*, Dey* et al. GCSC is a method for leveraging gene co-regulation to identify gene sets enriched for disease heritability, as described in our manuscript “Leveraging gene co-regulation to identify gene sets enriched for disease heritability” ( Siewert-Rocks et al. (July 2021) The GCSC software can be downloaded here. The S2G software can be used to estimate the precision and recall of SNP-to-gene linking (S2G strategies), and to construct combined S2G strategies to optimize their informativeness for disease risk, as described in our manuscript “Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity” ( Gazal et al. (August 2021) The S2G software can be downloaded here. scDRS is a method that links scRNA-seq with polygenic risk of disease at individual cell resolution, as described in our manuscript “Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data” ( Zhang*,Hou* et al. (September 2021) The scDRS software can be downloaded here. Tissue co-regulation score regression (TCSC) is a method that jointly analyzes GWAS and gene expression data to disentangle causal tissues from tagging tissues and partition disease heritability (or covariance between two diseases/traits) into tissue-specific components, as described in our manuscript “Modeling tissue co-regulation to estimate tissue specific contributions to disease” ( Amariuta et al. (August 2022) The TCSC software can be downloaded here. Further details are provided in our manuscript, “Age-dependent topic modelling of comorbidities in UK Biobank identifies disease subtypes with differential genetic risk” ( Jiang et al. The Age-dependent Topic Modeling (ATM) method provides a low-rank representation of longitudinal records of hundreds of distinct diseases in large EHR data sets, enabling the identification of disease subtypes based on heterogeneous comorbidity profiles. (January 2023) The ATM software can be downloaded here.

Software categories in east