Pinned

1. MAGE MAGE Public

   Analysis of gene expression and splicing diversity in a subset of samples from the 1000 Genomes Project, including eQTL and sQTL discovery and annotation.

   R 19

2. LD-PGTA LD-PGTA Public

   Linkage disequlibrium-informed PGT-A (LD-PGTA). A package for detecting genotypic signatures of aneuploidy from extremely low-coverage sequence data.

   Python 14

3. t2t-variants t2t-variants Public

   Code associated with the manuscript "A complete reference genome improves analysis of human genetic variation".

   R 15 3

4. LD-CHASE LD-CHASE Public

   A tool for linkage disequilibrium-informed comparison of haplotypes among sibling embryos.

   Python 3

5. sv_selection sv_selection Public

   Code for Yan et al., "Local adaptation and archaic introgression shape global diversity at human structural variant loci."

   R 5 2

6. rhapsodi rhapsodi Public

   R haploid sperm/oocyte data imputation (rhapsodi). A package for analysis of low-coverage single-cell sequencing data from multiple gametes.

   R 4