Structural variant caller for real-time long-read sequencing data

🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics

Plot structural variant signals from many BAMs and CRAMs

This repository contains implementations and illustrative code to accompany DeepMind publications

code to run sei and obtain sei and sequence class predictions

Short Tandem Repeat disease loci resource

Tool to annotate outfiles from ExpansionHunter and TRGT with the pathologic implications of the repeat

Copy number variant caller and depth visualization utility for PacBio HiFi reads

De novo tandem repeat calling from PacBio HiFi data

Tandem repeat genotyping and visualization from PacBio HiFi data

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.

What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.

pbsv - PacBio structural variant (SV) calling and analysis tools

An overview of all nanopack tools

A comprehensive analysis framework for Illumina methylation Beadchip

Gaussian Mixture Quantile Normalization (GMQN)

LongBow manuscript code repository

A fast library for AutoML and tuning. Join our Discord: https://discord.gg/Cppx2vSPVP.

A collection of resources to filter 'bad' probes from the Illumina 450k and EPIC methylation arrays

Illumina Human Methylation EPIC annotation to use with IlluminaHumanMethylationEPICB5manifest and minfi

Software package for assigning SARS-CoV-2 genome sequences to global lineages.

A Variant Call Format reader for Python.

Interface to use R from Python

Limma in Python

Scalable, Portable and Distributed Gradient Boosting (GBDT, GBRT or GBM) Library, for Python, R, Java, Scala, C++ and more. Runs on single machine, Hadoop, Spark, Dask, Flink and DataFlow

Download sequencing data and metadata from GSA, SRA, ENA, and DDBJ databases.

Harmonization of brain imaging features using bayesian inference