Pugh Lab (@pughlab)
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Top repositories

1

bamgineer

Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets
Python
36
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2

VisCap

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.
R
22
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3

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
21
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4

MEDIPIPE

HTML
9
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5

fragmentomics

Collection of fragmentomic analysis scripts
R
8
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6

crescent

The CanceR Single Cell ExpressioN Toolkit one-line-command applications.
R
8
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7

crescent-frontend

CReSCENT Portal: https://crescent.cloud | CReSCENT Docs: https://pughlab.github.io/crescent-frontend/
R
7
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8

inspire-genomics

Pan-cancer analysis of genomic and immune landscape profiles of metastatic solid tumors treated with pembrolizumab
R
7
star
9

su2c-gsc-scrna

Custom source code used in Richards, Whitley et al., Nature Cancer, 2021
Jupyter Notebook
7
star
10

oncographer

TypeScript
5
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11

tracker

Generic research tracking system
Java
5
star
12

LFS-early-detection-ctdna

Multi-modal analysis of cell-free DNA for the early detection of cancer in Li-Fraumeni syndrome.
R
5
star
13

cancer-scrna-integration

A comparison of data integration methods for single-cell RNA sequencing of cancer samples
Jupyter Notebook
4
star
14

cfMeDIP-seq-analysis-pipeline

Post-processing pipeline for next-generation circulating methylome data generated by cfMeDIP-seq
R
4
star
15

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
R
4
star
16

pipeline-suite

Collection of pipelines for NGS analysis along with utilities
Perl
3
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17

LB-Seq

Liquid Biopsy Sequencing analysis tools for cell free DNA sequencing
R
3
star
18

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.
R
3
star
19

scVkMYC_mPC

R
2
star
20

PughLabReadme

Documentation of best practices, coding tips, and ongoing projects developed by the Pugh Lab.
2
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21

TGL48_Uveal_Melanoma

scripts for uveal paper
R
2
star
22

BCa_ATACSEQ_Project

This repository contains custom code used for analysis in El Ghamrasni et al.,
R
2
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23

ctims

CTIMS project
CSS
2
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24

ped_CapTCRseq

Dynamics of peripheral T-cell repertoire in pediatric cancer patients over the course of chemoradiation
Jupyter Notebook
1
star
25

wnt-medulloblastoma-singh

Code for scRNAseq analysis in Manoranjan et al., Nature Communications, 2020
Jupyter Notebook
1
star
26

ddx56-pearson-lab

Code for scRNAseq analysis in Pryszlak et al., Cell Reports, 2021
Jupyter Notebook
1
star
27

cbio_import_utils

Python
1
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28

Clump

R
1
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29

net-seq

R
1
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30

mcoder

JavaScript
1
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31

TGL49_CHARM_LFS_Fragmentomics

R
1
star
32

cfmedip_analysis

Pre-processing pipeline to transform MEDIPS output wig files into matrix of chromosomal bins by samples
R
1
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33

btsc-glutaminase-weiss

Code for scRNAseq analysis in Restall et al., Cancer Research, 2020
R
1
star
34

paper-inspire-cfmedip

Accompanying code for INSPIRE cfMeDIP-seq manuscript
HTML
1
star