Brad Balderson's repositories
Cytocipher
Analysis methods for analysing single cell RNA-seq data; particularly with the goal of checking if tentative clusters of cells are significantly different to one another in terms of their gene expression.
Cytocipher_manuscript
Reproduces cytocipher manuscript results/figure panels.
Medulloblastoma
Primary analysis of Medulloblastoma PDX models for the paper: https://www.biorxiv.org/content/10.1101/2023.02.15.528116v1
SimpleNexusCaller
SimpleNexusCaller calls ChIP-nexus peaks based on the commonly provided bedGraph input format.
TreeMethods
Neighbour joining tree implementation.
avocado
Avocado is a multi-scale deep tensor factorization model that learns a latent representation of the human epigenome and enables imputation of epigenomic experiments that have not yet been performed.
BradBalderson.github.io
PhD student focusing on single cell genomics.
CellBender
CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
example_poag_hmtl
Example POAG
genomedata
The Genomedata format for storing large-scale functional genomics data.
hello-world
github
stLearn
A novel machine learning pipeline to analyse spatial transcriptomics data
hgvs
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
hyena-dna
Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena
Melanoma_manuscript
Contains code for figure panels and analysis for "Systematic analysis of the Transcriptional Landscape of Melanoma Reveals Drug-target Expression Plasticity"
NATMI
NATMI: Network Analysis Toolkit for the Multicellular Interactions