parklab/mutagenesis_tools

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Created over 5 years ago
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parklab/mutagenesis_tools

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Scripts for simulating mutant peptides and reading frames from mutations

NGSCheckMate

Software program for checking sample matching for NGS data

bamsnap

xTea

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

nozzle

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

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)

PaSDqc

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

scan-snv

Single cell somatic genotyper

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)

Salamander

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

HiTea

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

focal-amplification

HiScanner

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.

Jupyter Notebook

r-scansnv

R package for SCAN-SNV

comparative-website

Comparative modENCODE/ENCODE website.