Park Lab at Harvard Medical School

Repositories

• HiTea

  computational tool to identify trasposable element insertions using Hi-C data
  Perl MIT 3 3 0 0 Updated Sep 16, 2020

• bamsnap
  Python MIT 1 5 0 0 Updated Sep 15, 2020

• MosaicForecast

  A mosaic detecting software based on phasing and random forest
  Python MIT 13 31 0 1 Updated Aug 21, 2020

• ShatterSeek
  TeX 8 20 3 1 Updated Aug 19, 2020

• xTea

  (Pre-release)Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics

  software illumina transposable-elements paired-end linked-reads long-read-sequencing
  Python 0 4 0 0 Updated Aug 14, 2020

• NGSCheckMate

  Software program for checking sample matching for NGS data
  Python MIT 29 63 12 2 Updated May 28, 2020

• SigMA

  Mutational signature analysis for low statistics SNV data
  R 13 37 7 0 Updated Apr 30, 2020

• HiNT

  HiC for copy Number variation and Translocation detection
  Python 5 13 8 0 Updated Feb 17, 2020

• NGSAnalyses_WinstonLab

  The repository contains scripts used for analyzing Winston lab datasets
  R 1 1 0 0 Updated Nov 26, 2019

• scan-snv

  Single cell somatic genotyper
  Python 0 5 4 0 Updated Nov 8, 2019

• MSIprofiler

  Repo that aids in the detection of microsatellite instabilities (MSI) from sequencing data
  Python 2 15 0 0 Updated Oct 3, 2019

• LiRA
  R 2 10 2 1 Updated May 17, 2019

• r-scansnv

  R package for SCAN-SNV
  R 0 0 0 0 Updated May 3, 2019

• SCGenotyper_mini

  A lightweight (largely) self-contained genotyper for SNVs in single-cell DNA-seq data.
  Python 0 0 0 0 Updated Jun 15, 2018

• PaSDqc

  A python library for single cell whole-genome sequencing quality evaluation
  Python MIT 2 7 3 0 Updated May 11, 2018

• Software-Issues

  This repo exists for users of ParkLab software to be able to submit issues and have them remediated.
  0 0 8 0 Updated Jul 25, 2017

• emsar

  EMSAR quantifies transcripts from RNA-seq data (Citation : Lee et al., BMC Bioinformatics 2015, 16:278, http://www.biomedcentral.com/1471-2105/16/278)
  C 1 9 1 0 Updated May 5, 2016

• nozzle

  Nozzle is a report generation toolkit for data analysis pipelines implemented in R.

  reproducible-research html-report gehlenborglab
  R 22 56 16 1 Updated Apr 2, 2016

• comparative-website

  Comparative modENCODE/ENCODE website.
  CSS MIT 1 1 0 0 Updated Mar 26, 2015

• swagger-ui

  Forked from swagger-api/swagger-ui

  Swagger UI is a dependency-free collection of HTML, Javascript, and CSS assets that dynamically generate beautiful documentation from a Swagger-compliant API.
  JavaScript 7,533 0 0 0 Updated Dec 28, 2014

• refinery-deployment
  Puppet 0 1 1 0 Updated Jul 30, 2014

• refinery-utility-visualization
  JavaScript 0 3 0 0 Updated Jul 2, 2014