Park Lab at Harvard Medical School

NGSCheckMate

Software program for checking sample matching for NGS data

bamsnap

xTea

Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics

ShatterSeek

SigMA

Mutational signature analysis for low statistics SNV data

MosaicForecast

A mosaic detecting software based on phasing and random forest

HiNT

HiC for copy Number variation and Translocation detection

MuSiCal

A comprehensive toolkit for mutational signature analysis

MSIprofiler

Repo that aids in the detection of microsatellite instabilities (MSI) from sequencing data

LiRA

SCAN2

SCAN2 is a somatic SNV and indel genotyper for single cells amplified by Primary Template-Directed Amplification (PTA)

Salamander

Salamander is a non-negative matrix factorization framework for signature analysis

scan-snv

Single cell somatic genotyper

HiTea

computational tool to identify trasposable element insertions using Hi-C data

focal-amplification

SCAN2_PTA_paper_2022

Scripts for replicating the analyses in Luquette et al. 2022

xTea_paper

Host the scripts, running commands, and results for the xTea paper.

HiScanner

Scanner output visualization tool

mutagenesis_tools

Scripts for simulating mutant peptides and reading frames from mutations

r-scansnv

R package for SCAN-SNV

code-share

Repository to host shared code for the lab

SCGenotyper_mini

A lightweight (largely) self-contained genotyper for SNVs in single-cell DNA-seq data.

kras_project

luquette-glia-analysis

Scripts for the glia project

mpnst_surveyor

r-mutenrich

Analyze distribution of somatic mutations with permutations as a background

r-scan2

R package supporting the SCAN2 pipeline

SVA_catalog

Host the SVA reference catalog

SVA_landscape_project

ViScanner

Scanner output visualization tool