parklab Goto Github PK

bamsnap

code-share

Repository to host shared code for the lab

comparative-website

Comparative modENCODE/ENCODE website.

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)

focal-amplification

hint

HiC for copy Number variation and Translocation detection

hiscanner

hitea

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

kras_project

lira

luquette-glia-analysis

Scripts for the glia project

mosaicforecast

A mosaic detecting software based on phasing and random forest

mpnst_surveyor

msiprofiler

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

musical

A comprehensive toolkit for mutational signature analysis

mutagenesis_tools

Scripts for simulating mutant peptides and reading frames from mutations

ngscheckmate

Software program for checking sample matching for NGS data

nozzle

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

pasdqc

A python library for single cell whole-genome sequencing quality evaluation

r-mutenrich

Analyze distribution of somatic mutations with permutations as a background

r-scan2

R package supporting the SCAN2 pipeline

r-scansnv

R package for SCAN-SNV

salamander

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

scan-snv

Single cell somatic genotyper

scan2

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

scan2_pta_paper_2022

Scripts for replicating the analyses in Luquette et al. 2022

scgenotyper_mini

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

shatterseek

sigma

Mutational signature analysis for low statistics SNV data

software-issues

This repo exists for users of ParkLab software to be able to submit issues and have them remediated.