longfeili5170

longfeili5170's Stars

• netbiolab/scHumanNet

  Analysis cell-type-specific functional gene network, with SCINET and HumanNetv3

  Language:C++397

• saeyslab/multinichenetr

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

  Language:HTML12814

• pinellolab/dictys

  Context specific and dynamic gene regulatory network reconstruction and analysis

  Language:Python11114

• dmcable/spacexr

  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics

  Language:HTML32773

• StatBiomed/SpatialDM

  Spatial direct messaging detected by bivariate Moran

  Language:Jupyter Notebook245

• aertslab/scenicplus

  SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.

  Language:Jupyter Notebook19232

• lhc17/HoloNet

  HoloNet. Reveal the holograph of functional communication events in spatial transcriptomics. Help understand how microenvironments shaping cellular phenotypes

  Language:Python213

• zhengrongbin/MEBOCOST

  A python-based package and software to predict metabolite mediated cell-cell communications by single-cell RNA-seq data

  7011

• rargelaguet/mouse_organogenesis_10x_multiome_publication

  Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""

  Language:Jupyter Notebook406

• welch-lab/VeloVAE

  Deep Generative Modeling of RNA Velocity

  Language:Jupyter Notebook356

• tanlabcode/CytoTalk

  A novel computational method for inferring cell-type-specific signaling networks using single-cell transcriptomics data for better characterization of cell-cell communication.

  Language:R3711

• GregorySchwartz/too-many-cells

  Cluster single cells and analyze cell clade relationships with colorful visualizations.

  Language:Haskell10618

• faryabib/too-many-cells

  Cluster single cells and analyze cell clade relationships with colorful visualizations.

  Language:Haskell453

• quadbio/Pando

  Multiome GRN inference.

  Language:R11421

• igraph/python-igraph

  Python interface for igraph

  Language:Python1.3k249

• scverse/squidpy

  Spatial Single Cell Analysis in Python

  Language:Python44884

• jbergenstrahle/STUtility

  Language:R4712

• ludvigla/STUtility_web_site

  Language:R123

• jiang-junyao/IReNA

  R package IReNA

  Language:R2612

• HectorRDB/condiments

  Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression

  Language:R255

• workflowr/workflowr

  Organize your project into a research website

  Language:R832106

• ewest11/Bipolar-Serial-SABER-FISH-Analysis

  Language:Shell1

• MarioniLab/miloR

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

  Language:R34723

• welch-lab/MultiVelo

  Multi-omic velocity inference

  Language:Python10711

• SONGDONGYUAN1994/PseudotimeDE

  A robust DE test method that accounts for the uncertainty in pseudotime inference

  Language:R3313

• cistrome/MIRA

  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.

  Language:HTML609

• OSU-BMBL/deepmaps

  Single-cell biological network inference using a heterogeneous graph transformer

  Language:HTML695

• Pinlyu3/IReNA-v2

  Constructing gene regulatory networks by integrating scRNA-seq and scATAC-seq data

  Language:R112

• zqfang/GSEApy

  Gene Set Enrichment Analysis in Python

  Language:Python583119

• hhcho/densvis

  Density-preserving data visualization tools den-SNE and densMAP

  Language:Python10913