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auto-gpt

An experimental open-source attempt to make GPT-4 fully autonomous.

bbknn

Batch balanced KNN

ccst

Cell clustering for spatial transcriptomics data with graph neural network

cellid

Gene signature extraction and cell-identity recognition at individual cell level from single-cell RNA-seq.

cmp3111m-software-engineering-group-b8

concerto-reproducibility

cytospace

CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data

dstg

Deconvoluting Spatial Transcriptomics Data through Graph-based Artificial Intelligence

ggsci

🦄 Scientific journal and sci-fi themed color palettes for ggplot2

graphscc

single-cell RNA-seq clustering

graphst

gseapy

Gene Set Enrichment Analysis in Python

init

:exclamation: Go to the first (initial) commit of any GitHub repo

omicverse

A python library for multi omics included bulk and single cell RNA-seq analysis.

rapids-single-cell-examples

Examples of single-cell genomic analysis accelerated with RAPIDS

rapids_singlecell

Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data processing and analysis.

scadapt

scanpy

Single-cell analysis in Python. Scales to >1M cells.

scanpy-tutorials

Scanpy Tutorials.

scdior

scDIOR: Single cell data IO softwaRe

sceasy

A package to help convert different single-cell data formats to each other

scfea

single cell Flux Estimation Analysis (scFEA) Try the below web server!

scvi-tools

Deep probabilistic analysis of single-cell omics data

segment-anything

The repository provides code for running inference with the SegmentAnything Model (SAM), links for downloading the trained model checkpoints, and example notebooks that show how to use the model.

segment-everything-everywhere-all-at-once

Official implementation of the paper "Segment Everything Everywhere All at Once"

spagcn

SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network

spatialbenchmarking

squidpy

Spatial Single Cell Analysis in Python

squidpy_notebooks

Tutorials for Squidpy

tensorexpand

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