BradBalderson

BradBalderson's Stars

• clementchadebec/benchmark_VAE

  Unifying Variational Autoencoder (VAE) implementations in Pytorch (NeurIPS 2022)

  Language:Python1.8k163

• atarashansky/SCTransformPy

  A python port of the R package SCTransform:

  Language:Jupyter Notebook195

• gui11aume/starcode

  All pairs search and sequence clustering

  Language:C9021

• Noble-Lab/Sunbear

  single cell multimodal/multicondition temporal model

  Language:Python1

• BiomedicalMachineLearning/stlearn_manuscript

  Codes for generating stlearn figures

  Language:Jupyter Notebook51

• ArianeMora/SiRCle_multiomics_integration

  Language:HTML1

• scverse/pertpy

  Perturbation Analysis in the scverse ecosystem.

  Language:Python13921

• patfiaux/RELICS

  Regulatory Element Location Identification in CRISPR screens

  Language:R42

• lucidrains/enformer-pytorch

  Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

  Language:Python42579

• mcvickerlab/GenVarLoader

  Pipeline for efficient genomic data processing.

  Language:Python192

• hakyimlab/PrediXcan

  PrediXcan Project

  Language:Python10558

• fratajcz/speos

  A positive-unlabeled ensemble learning framework for disease gene prioritization.

  Language:Python142

• BradBalderson/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.

  Language:Jupyter Notebook306

• daniel-munro/ratgtex-pipeline

  Analysis pipeline for RatGTEx

  Language:Python3

• mcvickerlab/WASP2

  Allele-specific pipeline for unbiased read mapping(WIP), QTL discovery(WIP), and allelic-imbalance analysis

  Language:Python6

• instadeepai/nucleotide-transformer

  🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics

  Language:Python46855

• artidoro/qlora

  QLoRA: Efficient Finetuning of Quantized LLMs

  Language:Jupyter Notebook10k820

• probabilistic-learning/HI-VAE

  Language:Python8725

• neurogenomics/orthogene

  🧬 o r t h o g e n e 🧬✨✨✨✨✨✨✨ Interspecies gene mapping✨✨✨✨✨ 🦠 🔁 🌱 🔁 🌳 🔁 🍎 🔁 🍊 🔁 🪱 🔁 🪰 🔁 🐟 🔁 🦎 🔁 🐓 🔁 🦇 🔁 🐄 🔁 🐖 🔁 🐐 🔁 🐎 🔁 🐈 🔁 🐕 🔁 🐁 🔁 🐒 🔁 🦧 🔁 🦍 🔁 🏃‍♀️

  Language:R404

• wheaton5/souporcell

  Clustering scRNAseq by genotypes

  Language:Python16646

• limix/CellRegMap

  CellRegMap: A statistical framework for mapping context-specific regulatory variants using scRNA-seq

  Language:Python213

• yjzhang/split-seq-pipeline

  Language:Python2021

• Teichlab/scg_lib_structs

  Collections of library structure and sequence of popular single cell genomic methods

  Language:HTML42889

• WRiegs/V-finder

  A tool that automatically finds overlapping clinvar variants with Transcription Factor Binding Sights from the ReMAP2022 database.

  Language:Python2

• jon-xu/scSplit

  Genotype-free demultiplexing of pooled single-cell RNA-Seq, using a hidden state model for identifying genetically distinct samples within a mixed population.

  Language:Python409

• sebp/scikit-survival

  Survival analysis built on top of scikit-learn

  Language:Python1.1k214

• woojunshim/TRIAGE

  Transcriptional Regulatory Inference Analysis from Gene Expression (TRIAGE)

  Language:R9

• HazyResearch/hyena-dna

  Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena

  Language:Assembly58982

• ML4GLand/SeqPro

  Genomic sequence preprocessing toolkit

  Language:Python81

• ML4GLand/SeqData

  Annotated sequence data

  Language:Jupyter Notebook101