single-cell-omics

There are 53 repositories under single-cell-omics topic.

  • saeyslab/nichenetr

    NicheNet: predict active ligand-target links between interacting cells

    Language:R46914284117

  • zhanghao-njmu/SCP

    An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.

    Language:R362812380

  • genecell/single-cell-papers-with-code

    Papers with code for single cell related papers

    26512069

  • dynverse/dyno

    Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕

    Language:R166812232

  • dynverse/dynverse

    A set of tools supporting the development, execution, and benchmarking of trajectory inference methods. 🌍

    Language:R728415

  • dynverse/dyngen

    Simulating single-cell data using gene regulatory networks 📠

    Language:HTML703396
  • MAGMA_Celltyping

    neurogenomics/MAGMA_Celltyping

    Find causal cell-types underlying complex trait genetics

    Language:R70513831

  • prabhakarlab/Banksy

    BANKSY: spatial clustering

    Language:R6543412

  • xmc811/Scillus

    R Package for Single-Cell Dataset Processing and Visualization

    Language:R5342810

  • statgen/popscle

    A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools

    Language:C++4397215

  • RabadanLab/randomly

    A Library for Denoising Single-Cell Data with Random Matrix Theory

    Language:Jupyter Notebook3617410

  • MICS-Lab/scyan

    Biology-driven deep generative model for cell-type annotation in cytometry. Scyan is an interpretable model that also corrects batch-effect and can be used for debarcoding or population discovery.

    Language:Python333101
  • CellScopes.jl

    HaojiaWu/CellScopes.jl

    A Julia package for single cell and spatial data analysis

    Language:Julia274112

  • paulranum11/SPLiT-Seq_demultiplexing

    An unofficial demultiplexing strategy for SPLiT-seq RNA-Seq data

    Language:Python268108

  • multitalk/awesome-cell-cell-communication

    Collection of computational tools for cell-cell communication inference for single-cell and spatially resolved omics

    Language:Jupyter Notebook24205

  • caokai1073/Pamona

    The software of Pamona, a partial manifold alignment algorithm.

    Language:Jupyter Notebook19143

  • PixelgenTechnologies/pixelator

    A command-line tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) assays.

    Language:Python14401

  • lab-conrad/resVAE

    resVAE is a restricted latent variational autoencoder that we wrote to uncover hidden structures in gene expression data, especially using single-cell RNA sequencing. In principle it can be used with any hierarchically structured data though, so feel free to play around with it.

    Language:Jupyter Notebook12214

  • Terkild/CITE-seq_optimization

    Code and results from TotalSeqC antibody titration and pipeline benchmarking for CITE-seq experiments

    Language:R9202

  • nf-core/pixelator

    Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)

    Language:Nextflow8149243

  • yezhenqing/spatial-live

    A Lightweight & Versatile Visualization Tool for Spatial-Omics Data

    Language:TypeScript7100

  • davismcc/fibroblast-clonality

    Website for the fibroblast clonality project conducted at EMBL-EBI and the Wellcome Sanger Institute ca 2017-2019.

    Language:R6203

  • Cajun-data/nanoSPLITS

    Github repository for nanoSPLITS manuscript data and R scripts

    Language:HTML5110

  • shuzwang/P2_cochlea

    It contains the functional code to analyze P2 scRNA-seq and scATAC-seq data.

    Language:R5200

  • TheHumphreysLab/CellScopes.jl

    A Julia package for single cell and spatial data analysis

    Language:Julia5001

  • Catchxu/ACSleuth

    Domain Adaptive and Fine-grained Anomaly Detection for Single-cell Sequencing Data and Beyond

    Language:Python4102

  • talipucar/DomainTranslation

    Pytorch implementation of "Multi-domain translation between single-cell imaging and sequencing data using autoencoders" (https://www.nature.com/articles/s41467-020-20249-2) with custom models.

    Language:Python3100

  • aron0093/cy2path

    Factorial latent dynamic models trained on Markovian simulations of biological processes using single cell RNA sequencing data.

    Language:Python2100

  • dn070017/CAVACHON

    Cell cluster Analysis with Variational Autoencoder using Conditional Hierarchy Of latent representioN

    Language:Python1210

  • Flysta3D/multi_omics_atlas

    Custom codes for Flysta3D paper.

    Language:Python1110

  • HubINEM/RNAvelocity

    RNA velocity is a high-dimensional vector that predicts the future state of individual cells on a timescale of hours.

    Language:Jupyter Notebook1100

  • OpenOmics/cell-seek

    One single-cell pipeline to rule them all, one pipeline to find them, one pipeline to unify them all, and with the data bind them.

    Language:Python1100

  • poloarol/awesome-computational-biochemistry

    Papers and Tools that would guide your journey in Computational Biochemistry

    1200

  • royfrancis/seqhub

    Guide and links related to bulk and single-cell RNA-Seq experiments.

    Language:TeX130

  • saezlab/ccc_protocols

    LIANA x Tensor-cell2cell Protocols

    Language:Jupyter Notebook14163

  • SlavovLab/QuantQC

    QuantQC is a package for quality control (QC) of single-cell proteomics data. It is optimized to work with nPOP, a method for massively parallel sample preparation on glass slides.

    Language:HTML1101