wolfQK

LSGI

Local Spatial Gradient Inference

scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

Cell_Classification

MLP Cell_Classification

COMMOT

annoy

Approximate Nearest Neighbors in C++/Python optimized for memory usage and loading/saving to disk

flowsig

Python package to find communication-driven intercellular flows from single-cell RNA-sequencing and spatial transcriptomics data.

spateo-release

Spatiotemporal modeling of spatial transcriptomics

LISTA

Codes used in LISTA project.

MAGIC

MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.

magic

MAGIC - imputation and de-noising single-cell RNA seq data sets

Hotspot

REGSTA-script

omnipose

Omnipose: a high-precision solution for morphology-independent cell segmentation

qupath

QuPath - Bioimage analysis & digital pathology

CellProfiler

An open-source application for biological image analysis

VNS

A Novel Variable Neighborhood Search Approach for Cell Clustering Using Gene Expression and Spatial Coordinates

BatchEval

BatchEval: An Exquisite Workflow for Evaluating Batch Effects in Data Integration

SGAE

EAGS

EAGS:efficient and adaptive Gaussian smoothing

STCellbin

Enhanced application on generating single-cell gene expression profile for high-resolution spatial transcriptomics.

cellpose

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

miniforge

A conda-forge distribution.

docker-stacks

Ready-to-run Docker images containing Jupyter applications

DNBelab_C_Series_HT_scRNA-analysis-software

An open source and flexible pipeline to analysis high-throughput DNBelab C Series single-cell RNA datasets

stardist

StarDist - Object Detection with Star-convex Shapes

Scissor

Scissor package

awesome-spatial-data-analysis

Awesome list of tools and methods to perform spatial transcriptomic data analysis.

CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics

metapi

A general metagenomics data mining system focus on robust microbiome research

seqkit

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation