single-cell-omics

There are 57 repositories under single-cell-omics topic.

  • saeyslab/nichenetr

    NicheNet: predict active ligand-target links between interacting cells

    Language:R50414291119
  • zhanghao-njmu/SCP

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

    Language:R422813190
  • genecell/single-cell-papers-with-code

    Papers with code for single cell related papers

  • dynverse/dyno

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

    Language:R173812532
  • prabhakarlab/Banksy

    BANKSY: spatial clustering

    Language:R8243612
  • MAGMA_Celltyping

    neurogenomics/MAGMA_Celltyping

    Find causal cell-types underlying complex trait genetics

    Language:R77514231
  • dynverse/dyngen

    Simulating single-cell data using gene regulatory networks 📠

    Language:HTML733406
  • dynverse/dynverse

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

    Language:R738415
  • xmc811/Scillus

    R Package for Single-Cell Dataset Processing and Visualization

    Language:R6142810
  • 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++4397316
  • 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:Julia314132
  • multitalk/awesome-cell-cell-communication

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

    Language:Jupyter Notebook30205
  • paulranum11/SPLiT-Seq_demultiplexing

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

    Language:Python268108
  • 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:Python14412
  • 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
  • gao-lab/DECIPHER

    DECIPHER for learning high-fidelity disentangled embeddings from spatial omics data

    Language:Python110
  • Terkild/CITE-seq_optimization

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

    Language:R9202
  • tudaga/LabelCorrection

    Python code for cross-condition label refinement in single-cell data with HiDDEN

    Language:Jupyter Notebook9111
  • nf-core/pixelator

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

    Language:Nextflow8153244
  • yezhenqing/spatial-live

    A Lightweight & Versatile Visualization Tool for Spatial-Omics Data

    Language:TypeScript7100
  • Cajun-data/nanoSPLITS

    Github repository for nanoSPLITS manuscript data and R scripts

    Language:HTML6110
  • davismcc/fibroblast-clonality

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

    Language:R6203
  • TheHumphreysLab/CellScopes.jl

    A Julia package for single cell and spatial data analysis

    Language:Julia6001
  • shuzwang/P2_cochlea

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

    Language:R5200
  • Catchxu/ACSleuth

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

    Language:Python4102
  • deepomicslab/SCOIT

    SCOIT is an implementation of a probabilistic tensor decomposition framework for single-cell multi-omics data integration.

    Language:Python3221
  • 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:Python2210
  • poloarol/awesome-computational-biochemistry

    Papers and Tools that would guide your journey in Computational Biochemistry

  • 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:HTML2111
  • Flysta3D/multi_omics_atlas

    Custom codes for Flysta3D paper.

    Language:Python1110
  • fungenomics/NB-FOXR2

    Analysis for "FOXR2 targets LHX6+/DLX+ neural lineages to drive CNS neuroblastoma" (Jessa*, De Cola*, Chandarana*, et al, Cancer Research, 2024)

    Language:HTML1300