River366

kallisto

Near-optimal RNA-Seq quantification

ega-download-client

A Python-based EGA download client

hdWGCNA

High dimensional weighted gene co-expression network analysis

scDML

Batch alignment of single-cell transcriptomics data using deep metric learning

NeuronChat

DISCOtoolkit

cellDancer

Predict RNA velocity through deep learning

COSGR

Accurate and fast cell marker gene identification with COSG

gpt_academic

为GPT/GLM等LLM大语言模型提供实用化交互接口，特别优化论文阅读/润色/写作体验，模块化设计，支持自定义快捷按钮&函数插件，支持Python和C++等项目剖析&自译解功能，PDF/LaTex论文翻译&总结功能，支持并行问询多种LLM模型，支持chatglm3等本地模型。接入通义千问, deepseekcoder, 讯飞星火, 文心一言, llama2, rwkv, claude2, moss等。

HLCA

single-cell-papers-with-code

Papers with code for single cell related papers

HEU_KMS_Activator

CuratedAtlasQueryR

Tidy R query API for the harmonised and curated CELLxGENE single-cell atlas.

FIRM

Flexible Integration of single-cell RNA-sequencing data for large-scale Multi-tissue cell atlas datasets

scINSIGHT

Matrix factorization model for interpreting single cell gene expression in biologically heterogeneous data

GseaVis

An implement R package to visualize GSEA results

scRNAtoolVis

Useful functions to make your scRNA-seq plot more cool!

Scissor

Scissor package

scCancer

A package for automated processing of single cell RNA-seq data in cancer

PanCancer

Data available at: https://www.dropbox.com/sh/jh4s57kgbb0rnxe/AABoMK466cGc1OKsOuFN10wca?dl=0 and https://nyulangone-my.sharepoint.com/:f:/g/personal/dalia_barkley_nyulangone_org/EuHetdAOc2pLjm9XUwqdWicBnlXIbyvHx-EOC-inP-SGUg?e=rxa7Ry

velocyto.py

RNA velocity estimation in Python

FastIntegration

FastIntegrate integrates thousands of scRNA-seq datasets and outputs batch-corrected values for downstream analysis

scvelo

RNA Velocity generalized through dynamical modeling

pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

cNMF

Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data

sceasy

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

progeny

R package for Pathway RespOnsive GENe activity inference

sra-tools

SRA Tools

scanpy

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

MURP

A model-based downsampling algorithm for single-cell