medchenhao

cols4all

Colors for all (R package)

scgmt

Integrating multiple single cell rank-based gene set enrichment analysis together and multiple visual display methods.

scGSVA

scGSVA: Perform GSVA for single cell RNA seq

miloR

R package implementation of Milo for testing for differential abundance in KNN graphs

BioNERO

Easy and comprehensive biological network reconstruction and analysis

GeneCooc

BioEnricher

Integrate Analysis and Visualization for Bioinformatic Enrichment Analyzer

ggVolcano

The goal of `ggVolcano` is to help users make a beautiful volcano map more easily, including general volcano plot(`ggvolcano`), gradient color volcano plot(`gradual_volcano`) and GO term volcano plot(`term_volcano`).

scDrugPrio

Network analyses of single cell-based digital twins for personalized treatment of inflammatory disease

scFEA

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

decontPro

Recapitulates analysis for decontPro manuscript

clusterProfiler

:bar_chart: A universal enrichment tool for interpreting omics data

omicverse

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

signac

R toolkit for the analysis of single-cell chromatin data

ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

VPN

Yuko冲浪室之防迷路指南~

celda

Bayesian Hierarchical Modeling for Clustering Single Cell Genomic Data

Scillus

R Package for Single-Cell Dataset Processing and Visualization

scanpy

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

CellBender

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

decontX

Methods for decontamination of single cell data

SoupX

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data

popsicleR

popsicleR, a flexible R package aimed at providing most of the necessary quality controls and preliminary information for complete and detailed analysis of single cell RNA-seq data.

DoubletDecon

A tool for removing doublets from single-cell RNA-seq data

Chord

remove single cells Doublets by integrating tools!

scDblFinder

Methods for detecting doublets in single-cell sequencing data

scutilsR

ProjectSVR

A package for reference mapping and nice visualization

scMuscle

The Cornell Single-Cell Muscle Project (scMuscle) aims to collect, analyze and provide to the research community skeletal muscle transcriptomic data