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ARTISTA

Axolotl Regenerative Telencehpalon Interpretation via Spatiotemporal Transcriptomic Atlas

scimilarity

A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to represent new studies without additional training.

scPROTEIN

GBmap

Code used to create the core and extended GBmap, including downstream analyses (cell-cell interactions, spatial transcriptomics deconvolution) and how to produce the figures.

GPTCelltype

qiime2

Official repository for the QIIME 2 framework.

collapse

Advanced and Fast Data Transformation in R

SpatialMetaTranscriptomics

CellScopes.jl

A Julia package for single cell and spatial data analysis

comflowyspace

Comflowyspace is an intuitive, user-friendly, open-source AI tool for generating images and videos, democratizing access to AI technology.

gcap-wes

hypoMap_paper

A public clone of the HypoMap Figure & analysis repository.

multinichenetr

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

harmonypy

🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.

review-2023

二〇二三年的年终总结都写好了吗？

SPATA2

A Toolbox for Spatial Gene Expression Analysis

llm-course

Course to get into Large Language Models (LLMs) with roadmaps and Colab notebooks.

PanDepth

An ultra-fast and efficient genomic tool for coverage calculation

CMplot

📊 Circular and Rectangular Manhattan Plot

istar

kana

Single cell analysis in the browser

cellxgene_VIP

Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.

cellar

Interactive software tool for the assignment of cell types in single-cell studies.

scviewer

a lightweight single cell visualisation tool

cellenium

Cellenium is a FAIR and scalable interactive visual analytics app for scRNA-Seq data (single-cell RNA sequencing).

pypiper

Python toolkit for building restartable pipelines

simpleCache

Simplified R caching for reproducible big data projects

kana

Single cell analysis in the browser

spatialview

scCURE