pughlab/VisCap

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R
Created over 9 years ago
Updated almost 5 years ago

pughlab/VisCap

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VisCap is an open flexible, software program targeted to clinical laboratories for inference and visualization of germline copy number variants (CNVs) from targeted next-generation sequencing data. For algorithmic details, see Pugh TJ et al. Genet Med. 2016 Jul;18(7):712-9.

bamgineer

Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets

ConsensusCruncher

ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifiers (UMIs) to amalgamate reads derived from the same DNA template into a consensus sequence.

Jupyter Notebook

MEDIPIPE

fragmentomics

Collection of fragmentomic analysis scripts

su2c-gsc-scrna

Custom source code used in Richards, Whitley et al., Nature Cancer, 2021

Jupyter Notebook

inspire-genomics

Pan-cancer analysis of genomic and immune landscape profiles of metastatic solid tumors treated with pembrolizumab

crescent

The CanceR Single Cell ExpressioN Toolkit one-line-command applications.

crescent-frontend

CReSCENT Portal: https://crescent.cloud | CReSCENT Docs: https://pughlab.github.io/crescent-frontend/

LFS-early-detection-ctdna

Multi-modal analysis of cell-free DNA for the early detection of cancer in Li-Fraumeni syndrome.

oncographer

tracker

Generic research tracking system

inspire-ctdna

Custom R scripts for data visualization and statistical analysis for Bratman, Yang et al. 2020 Personalized circulating tumor DNA analysis as a predictive biomarker in solid tumor patients treated with pembrolizumab

cancer-scrna-integration

A comparison of data integration methods for single-cell RNA sequencing of cancer samples

Jupyter Notebook

cfMeDIP-seq-analysis-pipeline

Post-processing pipeline for next-generation circulating methylome data generated by cfMeDIP-seq

pipeline-suite

Collection of pipelines for NGS analysis along with utilities

LB-Seq

Liquid Biopsy Sequencing analysis tools for cell free DNA sequencing

VisCapCancer

Tool for calling tumour-specific somatic copy number alterations from targeted sequencing data. This tool is based on the germline copy number variant caller published by Pugh TJ et al. Genet Med. 2016 Jul;18(7):712-9.

scVkMYC_mPC

TGL48_Uveal_Melanoma

scripts for uveal paper

PughLabReadme

Documentation of best practices, coding tips, and ongoing projects developed by the Pugh Lab.

BCa_ATACSEQ_Project

This repository contains custom code used for analysis in El Ghamrasni et al.,

ctims

ped_CapTCRseq

Dynamics of peripheral T-cell repertoire in pediatric cancer patients over the course of chemoradiation

Jupyter Notebook

wnt-medulloblastoma-singh

Code for scRNAseq analysis in Manoranjan et al., Nature Communications, 2020

Jupyter Notebook

cbio_import_utils

ddx56-pearson-lab

Code for scRNAseq analysis in Pryszlak et al., Cell Reports, 2021

Jupyter Notebook

Clump

net-seq

mcoder

HCC_cfMeDIP

TGL49_CHARM_LFS_Fragmentomics

cfmedip_analysis

Pre-processing pipeline to transform MEDIPS output wig files into matrix of chromosomal bins by samples

btsc-glutaminase-weiss

Code for scRNAseq analysis in Restall et al., Cancer Research, 2020

paper-inspire-cfmedip

Accompanying code for INSPIRE cfMeDIP-seq manuscript