bradbalderson Goto Github PK

asr

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.

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.

example_poag_hmtl

Example POAG

genomedata

The Genomedata format for storing large-scale functional genomics data.

hello-world

github

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

mea_poa

medulloblastoma

Primary analysis of Medulloblastoma PDX models for the paper: https://www.biorxiv.org/content/10.1101/2023.02.15.528116v1

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

simplenexuscaller

SimpleNexusCaller calls ChIP-nexus peaks based on the commonly provided bedGraph input format.

stlearn

A novel machine learning pipeline to analyse spatial transcriptomics data

treemethods

Neighbour joining tree implementation.