parklab/MuSiCal

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31
Rank 820,005 (Top 17 %)
Language
Python
License
Other
Created over 3 years ago
Updated 4 months ago

parklab/MuSiCal

parklab

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A comprehensive toolkit for mutational signature analysis

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

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.

mutagenesis_tools

Scripts for simulating mutant peptides and reading frames from mutations