MONI: A Pangenomic Index for Finding MEMs

This repository contains codes and pipelines, as well as data used in the analysis of human inhibitory and excitatory neuronal clonal dynamics and lineage relationships, with cell-type-specific mos…

Command line and supplements for the project

Adaptation of Ginkgo (https://www.nature.com/articles/nmeth.3578) for CNV calling

A mosaic detecting software based on phasing and random forest

Deep learning framework for SV calling and genotyping

Black-capped and Carolina chickadees hybridize in the eastern United States, and hybrid chickadees have deficient learning and memory abilities. The goal of this project was to determine if cogniti…

A tool to detect postzygotic single-nucleotide mosaicism from unpaired, trio, or paired samples.

Nextflow pipeline for genome annotation of protein-coding genes

An automated RNA-seq pipeline using Nextflow

A list of alternative splicing analysis resources

rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis

SpliceWiz is an R package for exploring differential alternative splicing events in splice-aware alignment BAM files.

alternative splicing analysis pipeline

Tandem repeat genotyping with long reads

Tools for merging Tandem Repeat VCF files

Long Read Based SV Calling Tools Analysis

SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, and -DRB1 genes. Also, it supports both short- and long-read…

CLI tool for flexible and fast adaptive sampling on ONT sequencers

Nanopore long reads sequencing for clinical diagnosis

Construct Complex Table with knitr::kable() + pipe.

A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region expansions (RREs) from short DNA reads

ML and rule-based genome variant prioritization

MAGinator - Accurate SNV calling and profiling of MAGs

Exome Copy Number Variation Polisher via Deep Learning

Source code for the paper "The Effect of Kinship in Re-Identification Attacks Against Genomic Data Sharing Beacons"

Subset isotype-only vcf, build tree etc. steps after variant calling and isotype assignment

Concurrent identification of m6A and m5C modifications in individual molecules from nanopore sequencing

SUPPA: Fast quantification of splicing and differential splicing