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Stars8
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Rank 2,045,218 (Top 42 %)
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LanguageR
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Created almost 3 years ago
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Updated 11 months ago
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Repository Details
Collection of fragmentomic analysis scripts
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bamgineer
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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
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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
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MEDIPIPE
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crescent
The CanceR Single Cell ExpressioN Toolkit one-line-command applications.R
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crescent-frontend
CReSCENT Portal: https://crescent.cloud | CReSCENT Docs: https://pughlab.github.io/crescent-frontend/R
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inspire-genomics
Pan-cancer analysis of genomic and immune landscape profiles of metastatic solid tumors treated with pembrolizumabR
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su2c-gsc-scrna
Custom source code used in Richards, Whitley et al., Nature Cancer, 2021Jupyter Notebook
7
9
oncographer
TypeScript
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tracker
Generic research tracking systemJava
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LFS-early-detection-ctdna
Multi-modal analysis of cell-free DNA for the early detection of cancer in Li-Fraumeni syndrome.R
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12
cancer-scrna-integration
A comparison of data integration methods for single-cell RNA sequencing of cancer samplesJupyter Notebook
4
13
cfMeDIP-seq-analysis-pipeline
Post-processing pipeline for next-generation circulating methylome data generated by cfMeDIP-seqR
4
14
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 pembrolizumabR
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15
pipeline-suite
Collection of pipelines for NGS analysis along with utilitiesPerl
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16
LB-Seq
Liquid Biopsy Sequencing analysis tools for cell free DNA sequencingR
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17
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
18
scVkMYC_mPC
R
2
19
PughLabReadme
Documentation of best practices, coding tips, and ongoing projects developed by the Pugh Lab.
2
20
TGL48_Uveal_Melanoma
scripts for uveal paperR
2
21
BCa_ATACSEQ_Project
This repository contains custom code used for analysis in El Ghamrasni et al.,R
2
22
ctims
CTIMS projectCSS
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23
ped_CapTCRseq
Dynamics of peripheral T-cell repertoire in pediatric cancer patients over the course of chemoradiationJupyter Notebook
1
24
wnt-medulloblastoma-singh
Code for scRNAseq analysis in Manoranjan et al., Nature Communications, 2020Jupyter Notebook
1
25
ddx56-pearson-lab
Code for scRNAseq analysis in Pryszlak et al., Cell Reports, 2021Jupyter Notebook
1
26
cbio_import_utils
Python
1
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Clump
R
1
28
net-seq
R
1
29
mcoder
JavaScript
1
30
TGL49_CHARM_LFS_Fragmentomics
R
1
31
cfmedip_analysis
Pre-processing pipeline to transform MEDIPS output wig files into matrix of chromosomal bins by samplesR
1
32
btsc-glutaminase-weiss
Code for scRNAseq analysis in Restall et al., Cancer Research, 2020R
1
33
paper-inspire-cfmedip
Accompanying code for INSPIRE cfMeDIP-seq manuscriptHTML
1