Van Allen Lab

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65 repositories

pancan_germline_wgs
Public
Germline WGS variant calling across cancer types
R
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GNU General Public License v2.0
•0•0•0•1•Updated Mar 1, 2025Mar 1, 2025
get-oncotree-children
Public
Use the Oncotree API to fetch that version and, given a node, get child nodes
MIT License
•0•0•0•0•Updated Feb 28, 2025Feb 28, 2025
moalmanac-db
Public
Underlying content for the Molecular Oncology Almanac's database
precision-cancer-medicine molecular-oncology-almanac
GNU General Public License v2.0
•1•6•0•1•Updated Feb 28, 2025Feb 28, 2025
moalmanac-news
Public
GNU General Public License v2.0
•0•0•0•0•Updated Feb 26, 2025Feb 26, 2025
moalmanac-browser
Public
Web portal interface for browsing the Molecular Oncology Almanac
molecular-oncology-almanac python flask
Python
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GNU General Public License v2.0
•1•1•1•2•Updated Feb 26, 2025Feb 26, 2025
moalmanac-matchmaking
Public
Template repository to perform profile-to-cell line matchmaking
molecular-oncology-almanac
Python
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GNU General Public License v2.0
•0•0•3•0•Updated Feb 10, 2025Feb 10, 2025
moalmanac
Public
Molecular Oncology Almanac, a clinical interpretation algorithm paired with a novel underlying knowledge base for precision cancer medicine
python molecular-oncology-almanac precision-cancer-medicine clinical-interpretation-algorithm
HTML
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GNU General Public License v2.0
•5•16•1•1•Updated Feb 7, 2025Feb 7, 2025
clinicogenomics-FriendsDontLetFriends
Public
Directly inspired from Chenxin Li's "Friends Don't Let Friends Make Bad Graphs"
GNU General Public License v2.0
•0•0•0•0•Updated Feb 4, 2025Feb 4, 2025
germline-somatic-convergence
Public
Pilot exploration of overlap between germline and somatic alterations in common adult solid tumors
R
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GNU General Public License v2.0
•0•0•0•0•Updated Jan 29, 2025Jan 29, 2025
chek2_germline
Public
Analysis of germline genetic variants in CHEK2
WDL
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GNU General Public License v2.0
•0•0•0•0•Updated Jan 29, 2025Jan 29, 2025
beanie
Public
Tool for group biology estimation in single-cell RNAseq data
bioinformatics scrna-seq robustness subsampling gene-signatures signature-scoring differential-enrichment single-cell
Python
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GNU General Public License v2.0
•1•5•0•0•Updated Jan 8, 2025Jan 8, 2025
beanie-analysis
Public
Code for reproducing results presented in the BEANIE paper
Jupyter Notebook
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GNU General Public License v2.0
•0•0•0•0•Updated Jan 8, 2025Jan 8, 2025
miniconda
Public
Dockerfiles for Miniconda
Dockerfile
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GNU General Public License v2.0
•0•3•0•0•Updated Nov 5, 2024Nov 5, 2024
ped_germline_SV
Public
Analysis of germline SVs in pediatric cancers
Jupyter Notebook
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GNU General Public License v2.0
•1•2•0•0•Updated Oct 31, 2024Oct 31, 2024
comut
Public
CoMut is a Python library for visualizing genomic and phenotypic information via comutation plots
Python
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MIT License
•27•91•10•4•Updated Aug 1, 2024Aug 1, 2024
schadendorf-pd1
Public
code and data for Liu, Schilling, et al Nat Med 2019
Jupyter Notebook
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GNU General Public License v2.0
•6•18•1•0•Updated Aug 1, 2024Aug 1, 2024
SigProfilerAssignment-wrapper
Public
Implementation repository for SigProfilerAssignment
Python
•
GNU General Public License v2.0
•0•0•0•0•Updated Jul 12, 2024Jul 12, 2024
EAC-multiome
Public
Jupyter Notebook
•
MIT License
•0•0•0•0•Updated May 30, 2024May 30, 2024
terra-helper
Public
Terra storage helper
Python
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GNU General Public License v2.0
•0•0•4•2•Updated May 21, 2024May 21, 2024
moalmanac-paper
Public archive
Analyses related to Reardon et al. 2021, Integrating molecular profiles into clinical frameworks through the Molecular Oncology Almanac to prospectively guide precision oncology
paper precision-cancer-medicine molecular-oncology-almanac
HTML
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GNU General Public License v2.0
•4•5•0•1•Updated Mar 13, 2024Mar 13, 2024
pnet
Public
Implementation of P-Net as a flexible deep learning tool to generate insights from genetic features.
Jupyter Notebook
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GNU General Public License v2.0
•5•7•1•0•Updated Feb 12, 2024Feb 12, 2024
microhet-paper
Public
Jupyter Notebook
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GNU General Public License v2.0
•0•2•0•0•Updated Jan 17, 2024Jan 17, 2024
moalmanac-portal
Public
A cloud-based web portal for accessible clinical interpretation of integrative cancer genomics.
python flask molecular-oncology-almanac
HTML
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GNU General Public License v2.0
•3•1•3•5•Updated Oct 3, 2023Oct 3, 2023
.github
Public
About the Van Allen lab at Dana-Farber Cancer Institute
GNU General Public License v2.0
•0•0•0•0•Updated Sep 6, 2023Sep 6, 2023
2023-cgc
Public
Repository with notebook and slides for 2023 Cancer Genome Consortium workshop on the Molecular Oncology Almanac (moalmanac.org)
molecular-oncology-almanac
HTML
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GNU General Public License v2.0
•0•0•0•0•Updated Aug 13, 2023Aug 13, 2023
2017-aacr_phial2
Public
Computational analysis of clinically actionable genomic features: Precision Heuristics for Interpreting the Alteration Landscape (PHIAL) - AACR 2017
cancer vanallenlab broadinstitute hhmi danafarber precisionmedicine
Jupyter Notebook
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GNU General Public License v2.0
•0•1•0•0•Updated Feb 16, 2023Feb 16, 2023
2017-tcga-mc3_phial
Public
Cohort analysis of TCGA mc3 with PHIAL
Jupyter Notebook
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GNU General Public License v2.0
•1•2•0•0•Updated Feb 16, 2023Feb 16, 2023
peds_ctDNA
Public
Algorithm for quantifying the number of translocation reads and wild-type reads in plasma samples with detectable ctDNA
Shell
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GNU General Public License v2.0
•0•0•0•0•Updated Feb 16, 2023Feb 16, 2023
abs_maf_clustering_vis
Public
This workflow can be used to visualize the data from an *ABS_MAF.txt absolute file output. Both detection power and genomic locus are plotted for all SNPs, along with clustering information based on cancer cell fraction.
Python
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GNU General Public License v2.0
•2•1•0•0•Updated Feb 16, 2023Feb 16, 2023
maf_set_ops
Public
A class for calculating maf set intersections, with example scripts demonstrating usage.
Python
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GNU General Public License v2.0
•0•0•0•0•Updated Feb 16, 2023Feb 16, 2023