pughlab/ctims

CTIMS project

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pughlab/HCC_cfMeDIP

Language: R - Size: 207 KB - Last synced: about 19 hours ago - Pushed: about 21 hours ago - Stars: 1 - Forks: 0

pughlab/ORACLE_TCR

Language: R - Size: 50.8 KB - Last synced: 5 days ago - Pushed: 6 days ago - Stars: 0 - Forks: 0

pughlab/ped_CapTCRseq

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

Language: Jupyter Notebook - Size: 53.8 MB - Last synced: 2 days ago - Pushed: 6 days ago - Stars: 1 - Forks: 0

pughlab/oncographer

Language: TypeScript - Size: 85.1 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 5 - Forks: 1

pughlab/pipeline-suite

Collection of pipelines for NGS analysis along with utilities

Language: Perl - Size: 69.1 MB - Last synced: 20 days ago - Pushed: 21 days ago - Stars: 3 - Forks: 0

pughlab/INSPIRE_TCR

Pan-cancer assessment of the tumour and systemic T-cell receptor repertoire dynamics in patients treated with pembrolizumab

Language: R - Size: 3.03 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

pughlab/fragmentomics

Collection of fragmentomic analysis scripts

Language: R - Size: 827 KB - Last synced: about 1 month ago - Pushed: 11 months ago - Stars: 9 - Forks: 2

pughlab/inspire-genomics

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

Language: R - Size: 108 MB - Last synced: about 1 month ago - Pushed: 10 months ago - Stars: 7 - Forks: 1

pughlab/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.

Language: Jupyter Notebook - Size: 51.6 MB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 21 - Forks: 10

pughlab/paper-inspire-cfmedip

Accompanying code for INSPIRE cfMeDIP-seq manuscript

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pughlab/cfMeDIP-seq-analysis-pipeline

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

Language: R - Size: 22 MB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 4 - Forks: 2

pughlab/LFS-early-detection-ctdna

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

Language: R - Size: 9.25 MB - Last synced: about 1 month ago - Pushed: 11 months ago - Stars: 5 - Forks: 1

pughlab/GSoC

Google Summer of Code Ideas list

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pughlab/MEDIPIPE

Language: HTML - Size: 407 MB - Last synced: about 1 month ago - Pushed: 10 months ago - Stars: 9 - Forks: 2

pughlab/CNAqc Fork of caravagnalab/CNAqc

CNAqc - Copy Number Alteration (CNA) Quality Check package

Language: R - Size: 233 MB - Last synced: about 1 month ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

pughlab/cbioportal Fork of cBioPortal/cbioportal

cBioPortal for Cancer Genomics

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pughlab/scVkMYC_mPC

Language: R - Size: 112 KB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 2 - Forks: 0

pughlab/rascal Fork of crukci-bioinformatics/rascal

R package and Shiny app providing functions for scaling relative copy number to absolute values for shallow whole genome sequencing of cancer samples.

Language: R - Size: 3.73 MB - Last synced: about 1 month ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

pughlab/SRTPMs Fork of onermustafaumit/SRTPMs

Spatially Resolved Tumor Purity Maps (SRTPMs)

Language: Python - Size: 41.5 MB - Last synced: about 1 month ago - Pushed: 8 months ago - Stars: 0 - Forks: 0

pughlab/ctims-pages

CTIMS Github Pages

Size: 512 KB - Last synced: about 1 month ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

pughlab/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.

Language: R - Size: 28.3 KB - Last synced: about 1 month ago - Pushed: over 4 years ago - Stars: 22 - Forks: 12

pughlab/BCa_ATACSEQ_Project

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

Language: R - Size: 54.7 KB - Last synced: about 1 month ago - Pushed: about 3 years ago - Stars: 2 - Forks: 1

pughlab/su2c-gsc-scrna

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

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pughlab/TGL49_CHARM_LFS_Fragmentomics

Language: R - Size: 10.5 MB - Last synced: about 1 month ago - Pushed: 9 months ago - Stars: 1 - Forks: 0

pughlab/matchminer-api Fork of dfci/matchminer-api

A platform for matching patient-specific genomic profiles to precision cancer medicine clinical trials

Size: 5.4 MB - Last synced: 27 days ago - Pushed: 27 days ago - Stars: 0 - Forks: 0

pughlab/matchminer-api-v1 Fork of dfci/matchminer-api

A platform for matching patient-specific genomic profiles to precision cancer medicine clinical trials

Language: Python - Size: 14.3 MB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

pughlab/bamgineer

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

Language: Python - Size: 23.1 MB - Last synced: about 1 month ago - Pushed: almost 4 years ago - Stars: 36 - Forks: 12

pughlab/EVOLVE_ctDNA

code used for the analysis and visualization of the EVOLVE ctDNA project

Language: R - Size: 6.27 MB - Last synced: about 1 month ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

pughlab/cfmedip_analysis

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

Language: R - Size: 11.7 KB - Last synced: about 1 month ago - Pushed: almost 5 years ago - Stars: 1 - Forks: 0

pughlab/cbpOrganizer

Tool to help cbioportal study owners to organize their studies for publishing to cbioportal

Language: Python - Size: 196 KB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 0 - Forks: 1

pughlab/PughLabReadme

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

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pughlab/TGL48_Uveal_Melanoma

scripts for uveal paper

Language: R - Size: 53.3 MB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 2 - Forks: 0

pughlab/data-processor 📦

Script to convert from VCF files to MAF files ready to be imported into cBioPortal

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pughlab/cbioportal-documentation 📦

Size: 35.2 KB - Last synced: about 1 month ago - Pushed: about 8 years ago - Stars: 0 - Forks: 0

pughlab/tracker 📦

Generic research tracking system

Language: Java - Size: 2.04 MB - Last synced: about 1 month ago - Pushed: about 7 years ago - Stars: 5 - Forks: 1

pughlab/pughlab-document

Size: 1.95 KB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

pughlab/gitbook-labmanual

Size: 1000 Bytes - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

pughlab/iMATRIX-Atezo_Biomarker

Multimodal immunogenomic biomarker analysis of tumours from pediatric patients enrolled to a phase 1-2 study of single-agent atezolizumab

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pughlab/mcoder

Language: JavaScript - Size: 8.97 MB - Last synced: about 1 month ago - Pushed: 11 months ago - Stars: 1 - Forks: 0

pughlab/gitdemo

Repo for demo of git and github

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pughlab/plbr-docs

Size: 95.9 MB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

pughlab/myeloma-workflow-calc

Language: HTML - Size: 79.1 KB - Last synced: about 1 month ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

pughlab/CapTCR-TIL-Tracking

Language: R - Size: 251 MB - Last synced: about 1 month ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

pughlab/aneuploidy_score Fork of quevedor2/aneuploidy_score

R package to calculate the Aneuploidy Score from Chromosome Arm-level SCNAs/Aneuploidies (CAAs) as outlined and expanded by Shukla et al. (https://doi.org/10.1038/s41467-020-14286-0)

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pughlab/cancer-scrna-integration

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

Language: Jupyter Notebook - Size: 242 KB - Last synced: about 1 month ago - Pushed: almost 3 years ago - Stars: 4 - Forks: 1

pughlab/wnt-medulloblastoma-singh

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

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pughlab/bam2bedpe

convert bam to bedpe format

Language: Shell - Size: 37.1 KB - Last synced: about 1 month ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

pughlab/PLBR_MedRemixBEDPE

Run MedRemix with bedpe input as part of PLBR database workflow

Language: Python - Size: 10.1 MB - Last synced: about 1 month ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

pughlab/PLBR_MeDEStrandBEDPE

Run MeDEStrand with bedpe input as part of PLBR database workflow

Language: Shell - Size: 10.5 MB - Last synced: about 1 month ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

pughlab/immunogenomics_pedNST

Immunogenomics of pediatric nervous system tumours

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pughlab/cbioportal-docs

Size: 5.57 MB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

pughlab/mcoder-docs

Size: 1.65 MB - Last synced: about 1 month ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

pughlab/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.

Language: R - Size: 25.4 KB - Last synced: about 1 month ago - Pushed: over 3 years ago - Stars: 3 - Forks: 3

pughlab/crescent-frontend

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

Language: R - Size: 124 MB - Last synced: about 1 month ago - Pushed: about 2 years ago - Stars: 7 - Forks: 2

pughlab/getting-started

Size: 34.2 KB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

pughlab/methylation-signatures-resource

Shared methylation signatures resource

Size: 200 KB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

pughlab/crescent

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

Language: R - Size: 4.8 MB - Last synced: about 1 month ago - Pushed: 3 months ago - Stars: 8 - Forks: 4

pughlab/cbioportal-frontend Fork of cBioPortal/cbioportal-frontend

React Frontend of cBioPortal :tada:

Language: TypeScript - Size: 656 MB - Last synced: about 1 month ago - Pushed: 8 months ago - Stars: 1 - Forks: 1

pughlab/cbpManager Fork of arsenij-ust/cbpManager

Generate, manage and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics.

Size: 3.36 MB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

pughlab/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

Language: R - Size: 64.5 KB - Last synced: about 1 month ago - Pushed: over 3 years ago - Stars: 4 - Forks: 4

pughlab/cbio-auto-import

scripts used for auto importing new datasets into the cBioPortal database; live

Language: Python - Size: 53.7 KB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

pughlab/cbioportal-importer

python package to load cancer genomics data sets into the cbioportal database; not live

Language: Python - Size: 60.5 KB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

pughlab/import_wrapper

A small wrapper to help import to cBioPortal; not live

Language: Perl - Size: 1.86 MB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

pughlab/cbioportal-deployment

Stuff to help deploy cBioPortal with ansible

Language: Jinja - Size: 2.64 MB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 0 - Forks: 3

pughlab/matchengine-V2 Fork of dfci/matchengine-V2

Open source engine for matching cancer patients to precision medicine clinical trials (V2).

Size: 15 MB - Last synced: about 1 month ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

pughlab/net-seq

Language: R - Size: 72.9 MB - Last synced: about 1 month ago - Pushed: over 4 years ago - Stars: 1 - Forks: 0

pughlab/Genie-analysis Fork of Sage-Bionetworks/Genie-analysis

Analysis code (R, Python, SQL...) to assist with users interacting with the GENIE public data.

Size: 40 KB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

pughlab/GENIE_100K_Supp_Figure_S2

Code to generate Supplementary Figure S2 for GENIE 100K paper

Language: R - Size: 1.95 KB - Last synced: about 1 month ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

pughlab/swgs

Snakemake workflow for shallow WGS analysis

Language: Python - Size: 183 KB - Last synced: about 1 month ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 1

pughlab/WadingPool Fork of quevedor2/WadingPool

A shallow/low-pass whole-genome analaysis toolkit

Size: 184 KB - Last synced: about 1 month ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

pughlab/DeconPeaker Fork of elsamah/DeconPeaker

a deconvolution model to identify cell types based on chromatin accessibility in ATAC-Seq data of mixture samples

Size: 54.2 MB - Last synced: about 1 month ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

pughlab/NEAT Fork of ncsa/NEAT

Size: 75.1 MB - Last synced: about 1 month ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

pughlab/dunovo Fork of galaxyproject/dunovo

Reference-free duplex sequencing pipeline.

Language: Python - Size: 708 KB - Last synced: about 1 month ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

pughlab/ddx56-pearson-lab

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

Language: Jupyter Notebook - Size: 3.93 MB - Last synced: about 1 month ago - Pushed: about 3 years ago - Stars: 1 - Forks: 1

pughlab/btsc-glutaminase-weiss

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

Language: R - Size: 111 KB - Last synced: about 1 month ago - Pushed: over 3 years ago - Stars: 1 - Forks: 1

pughlab/GENIE-FMI-converter Fork of Sage-Bionetworks/GENIE-FMI-converter

This is the converter for foundation medicine provided by DUKE for GENIE

Language: Python - Size: 9.77 KB - Last synced: about 1 month ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

pughlab/SchramekLOH

Analysis for the ADAM10 and AJUBA LOH in HNSC

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pughlab/PLTK

Pughlab Toolkit (PLTK): Repository for all small analysis, plotting, preprocessing, and formatting scripts

Language: R - Size: 8.19 MB - Last synced: about 1 month ago - Pushed: over 3 years ago - Stars: 0 - Forks: 4

pughlab/immune-profiling

Language: Python - Size: 18.6 KB - Last synced: 2 days ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

pughlab/redcap-docs

Size: 0 Bytes - Last synced: about 1 month ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0

pughlab/session-service Fork of cBioPortal/session-service

Language: Java - Size: 113 KB - Last synced: about 1 month ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0

pughlab/trialmatchapi

Language: Java - Size: 29.8 MB - Last synced: about 1 month ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

pughlab/immds

Language: Python - Size: 8.79 KB - Last synced: about 1 month ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

pughlab/cbio_import_utils

Language: Python - Size: 39.1 KB - Last synced: about 1 month ago - Pushed: over 5 years ago - Stars: 1 - Forks: 1

pughlab/Labkey-API-Wrapper

Language: Python - Size: 533 KB - Last synced: about 1 month ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

pughlab/optimal_gamma_selector

A visual tool to explore a number of gamma values to find the optimal one for copy number segments.

Language: CSS - Size: 3.91 KB - Last synced: about 1 month ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

pughlab/matchminer-engine Fork of oncokb/matchminer-engine

Match genomic profiles to clinical trials

Language: Python - Size: 17.2 MB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

pughlab/MultiMMR

Language: R - Size: 2.93 KB - Last synced: about 1 month ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0

pughlab/matchminer-ui Fork of dfci/matchminer-ui

Language: JavaScript - Size: 919 KB - Last synced: about 1 month ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0

pughlab/Clump

Language: R - Size: 5.27 MB - Last synced: about 1 month ago - Pushed: almost 6 years ago - Stars: 1 - Forks: 0

pughlab/LB-Seq

Liquid Biopsy Sequencing analysis tools for cell free DNA sequencing

Language: R - Size: 19.5 KB - Last synced: about 1 month ago - Pushed: over 7 years ago - Stars: 3 - Forks: 5

pughlab/SPECIAL

Size: 0 Bytes - Last synced: about 1 month ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

pughlab/braf_rapid_autopsy

Computational analysis for BRAF-mutant melanoma rapid autopsy project

Language: JavaScript - Size: 8.03 MB - Last synced: about 1 month ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

pughlab/cbioportal-oidc-overlay

Language: Java - Size: 27.3 KB - Last synced: about 1 month ago - Pushed: about 7 years ago - Stars: 0 - Forks: 0

pughlab/java-server

Provides a Jetty-based server container for the tracker, cBioPortal, and others

Language: Java - Size: 42 KB - Last synced: about 1 month ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0

pughlab/cbioportal-octane-overlay

The OCTANE branding for cBioPortal, as a war overlay

Size: 120 KB - Last synced: about 1 month ago - Pushed: over 7 years ago - Stars: 0 - Forks: 1

pughlab/LB-Seq_data_visualization

Language: R - Size: 4.88 KB - Last synced: about 1 month ago - Pushed: almost 8 years ago - Stars: 0 - Forks: 1

pughlab/OpenIDConnect Fork of agmoyano/OpenIDConnect

A simple customizable OpenID Connect provider (server) for node.js.

Language: JavaScript - Size: 227 KB - Last synced: about 1 month ago - Pushed: almost 8 years ago - Stars: 0 - Forks: 0

pughlab/tracker-deployment

Language: Shell - Size: 55.7 KB - Last synced: about 1 month ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0