jiazhao97

DeepVelo

pykan

Kolmogorov Arnold Networks

ELD

XMAP

BINRES

vizgen-postprocessing

speckle

R package for analysing single cell data

GSEApy

Gene Set Enrichment Analysis in Python

DeepTCR

Deep Learning Methods for Parsing T-Cell Receptor Sequencing (TCRSeq) Data

conga

Clonotype Neighbor Graph Analysis

tradeSeq

TRAjectory-based Differential Expression analysis for SEQuencing data

PhenoGraph

Subpopulation detection in high-dimensional single-cell data

Beeline

BEELINE: evaluation of algorithms for gene regulatory network inference

cellpose

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

CCST

Cell clustering for spatial transcriptomics data with graph neural network

SCAMPR

Analysis pipeline for spatial high-dimensional in situ hybridization (HiPlex RNAScope)

stardist

StarDist - Object Detection with Star-convex Shapes

Nudiff

Diffusion-based Data Augmentation for Nuclei Image Segmentation

mermaid

Image registration using pytorch

registration

Image Registration

CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data

STalign

Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping

LongReadBenchmark

Benchmarking long-read RNA-seq analysis tools

torch-lddmm

GPU and CPU implementation of LDDMM image registration

pyLDDMM

Python Implementation of the LDDMM algorithm

FLAG

Flexible and Accurate Methods for Estimation and Inference of Gaussian Graphical Models with Applications

BWMR

BWMR (Bayesian Weighted Mendelian Randomization)

dipy

DIPY is the paragon 3D/4D+ imaging library in Python. Contains generic methods for spatial normalization, signal processing, machine learning, statistical analysis and visualization of medical images. Additionally, it contains specialized methods for computational anatomy including diffusion, perfusion and structural imaging.

Network-Response-Shrinkage-Model

ADDL

Apply deep learning on ADNI MRI for Alzheimer disease diagnostic.