Stars
Python applications and libraries for working with PGS data and the PGS Catalog
Polygenic Risk Scores Extension for Diabetes Mellitus (PRSedm)
Tools to convert Illumina IDAT/BPM/EGT/GTC and Affymetrix CEL/CHP files to VCF
Imputation Server 2 workflow to facilitate genotype imputation at scale.
Toolkit to aid generation of advanced Polygenic Risk Scores (PRS) including SNP-allele tagging and interaction models, especially in HLA. Developed and maintained by Seth Sharp ([email protected]).
This API provides programmatic access to the AlphaGenome model developed by Google DeepMind.
Read-based phasing of genomic variants, also called haplotype assembly
Tools for fast and flexible genome assembly scaffolding and improvement
Longread PacBio sequencing processing for WGS and PureTarget
Nanopore demultiplexing, QC and alignment pipeline
Fast, sensitive and accurate integration of single-cell data with Harmony
UCE is a zero-shot foundation model for single-cell gene expression data
Reference mapping for single-cell genomics
A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to represent new studies without additional training.
An interactive explorer for single-cell transcriptomics data
A single cell transcriptomics pipeline for QC, integration and making the data presentable
Tools for handling Unique Molecular Identifiers in NGS data sets
https://www.sc-best-practices.org
Applying polygenic scores (PGS) on imputed genotypes
Deep probabilistic analysis of single-cell and spatial omics data
Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"
Analysis pipleine to model tumour clonal evolution from WGS data (driver annotation, quality control of copy number calls, subclonal and mutational signature deconvolution)