abuchin
Genetics, Neuroscience, Single cell omics, Neural networks, Cell biophysics, Machine learning
@synthesizebio Seattle
Pinned Repositories
All-active-Manuscript
Code for reproducing the figures presented in: Single-neuron models linking electrophysiology, morphology and transcriptomics across cortical cell types
All-active-Workflow-v1
Creating the code base for All-active Model generation written on top of Bluepyopt
Ca-spike-extraction-and-SVM-decoder
ML spike algorithm and SVM decoder predicting the drifting gratings direction based on optical recordings in V1 visual cortex.
EI-with-adaptation
This code simulates the E-I population model in XPPAUT.
human-epilepsy-project
human_neuron_Ih
This repository contains the simulation code to run single neuron simulations in the early version of bmtk (https://github.com/AllenInstitute/bmtk)
jazz_lstm
LSTM for Jazz
Mouse-all-active-models-EAP
Mouse_V1_EAP_Analysis
human_neuron_Ih
This repository contains the simulation code to run single neuron simulations in the early version of bmtk (https://github.com/AllenInstitute/bmtk)
abuchin's Repositories
abuchin/epilepsy_human_dg
abuchin/human-epilepsy-project
abuchin/awesome-foundation-model-single-cell-papers
Copy of foundational model branch
abuchin/best-leetcode-resources
This repository contains resources for technical coding interviews.
abuchin/best-system-design-resources
This repository contains System Design Interview resources to design large-scale distributed systems.
abuchin/cellhint
A tool for semi-automatic cell type harmonization and integration
abuchin/cellpose
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
abuchin/clean-code-python
:bathtub: Clean Code concepts adapted for Python
abuchin/course22
The fast.ai course notebooks
abuchin/delve
Feature selection for preserving biological trajectories in single-cell data
abuchin/GEARS
GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations
abuchin/genformer
abuchin/gget
š§¬ gget enables efficient querying of genomic reference databases
abuchin/Great-Deep-Learning-Tutorials
A Great Collection of Deep Learning Tutorials and Repositories
abuchin/hyena-dna
A long-range genomic foundation model built with Hyena
abuchin/LABRAT
Lightweight Alignment Based Resolution of Alternative Three Prime Ends
abuchin/leafcutter
Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard
abuchin/Leaflet
Leaflet is a probabilistic model that identifies latent cell states defined by splicing changes.
abuchin/ML_protein_ligand_prediction
abuchin/paper-qa
LLM Chain for answering questions from documents with citations
abuchin/pertpy
Perturbation Analysis in the scverse ecosystem.
abuchin/perturbation_benchmarking
Comparing performance across many methodological dimensions among tools that predict RNA after TF knockdowns and overexpression.
abuchin/PyDESeq2
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
abuchin/sagemaker-ssh-helper
A helper library to connect into Amazon SageMaker with AWS Systems Manager and SSH (Secure Shell)
abuchin/scutrboot
Bootstrapping methods for 3' UTR analysis of scRNA-seq
abuchin/sinto
Tools for single-cell data processing
abuchin/sleuth
Differential analysis of RNA-Seq
abuchin/STAR
RNA-seq aligner
abuchin/ucdeconvolve
UniCell Deconvolve - Cloud Cell Type Deconvolution For Transcriptomic Data
abuchin/variancePartition
Quantify and interpret divers of variation in multilevel gene expression experiments