medchenhao

medchenhao's Stars

• scverse/scanpy

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

  Language:Python1.9k511.7k594

• YuLab-SMU/clusterProfiler

  :bar_chart: A universal enrichment tool for interpreting omics data

  Language:R99845632252

• Starlitnightly/omicverse

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

  Language:Jupyter Notebook39159945

• GreenleafLab/ArchR

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

  Language:R372151.1k132

• MarioniLab/miloR

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

  Language:R332924422

• stuart-lab/signac

  R toolkit for the analysis of single-cell chromatin data

  Language:R31661.2k85

• mtennekes/cols4all

  Colors for all (R package)

  Language:R30962817

• broadinstitute/CellBender

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

  Language:Python2791030950

• constantAmateur/SoupX

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

  Language:R254614635

• plger/scDblFinder

  Methods for detecting doublets in single-cell sequencing data

  Language:R15157818

• campbio/celda

  Bayesian Hierarchical Modeling for Clustering Single Cell Genomic Data

  Language:R148710428

• changwn/scFEA

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

  Language:Jupyter Notebook9215932

• EDePasquale/DoubletDecon

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

  Language:R6965419

• Zaoqu-Liu/BioEnricher

  Integrate Analysis and Visualization for Bioinformatic Enrichment Analyzer

  Language:HTML68398

• BioSenior/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`).

  Language:R643112

• Yuko-VPN/VPN

  Yuko冲浪室之防迷路指南~

  61269

• xmc811/Scillus

  R Package for Single-Cell Dataset Processing and Visualization

  Language:R5242810

• guokai8/scGSVA

  scGSVA: Perform GSVA for single cell RNA seq

  Language:R442263

• campbio/decontX

  Methods for decontamination of single cell data

  Language:R282161

• almeidasilvaf/BioNERO

  Easy and comprehensive biological network reconstruction and analysis

  Language:R242255

• bicciatolab/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.

  Language:R24547

• mckellardw/scMuscle

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

  Language:HTML181114

• 13308204545/Chord

  remove single cells Doublets by integrating tools!

  Language:R174

• JarningGau/ProjectSVR

  A package for reference mapping and nice visualization

  Language:R17230

• JarningGau/GeneCooc

  Language:R11110

• SDTC-CPMed/scDrugPrio

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

  Language:R9111

• JarningGau/scutilsR

  Language:R5201

• ShengFang-0829/scgmt

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

  Language:Jupyter Notebook31

• campbio-manuscripts/decontPro

  Recapitulates analysis for decontPro manuscript

  Language:R2