single-cell-omics
There are 57 repositories under single-cell-omics topic.
saeyslab/nichenetr
NicheNet: predict active ligand-target links between interacting cells
zhanghao-njmu/SCP
An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
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 🦕
prabhakarlab/Banksy
BANKSY: spatial clustering
neurogenomics/MAGMA_Celltyping
Find causal cell-types underlying complex trait genetics
dynverse/dyngen
Simulating single-cell data using gene regulatory networks 📠
dynverse/dynverse
A set of tools supporting the development, execution, and benchmarking of trajectory inference methods. 🌍
xmc811/Scillus
R Package for Single-Cell Dataset Processing and Visualization
statgen/popscle
A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools
RabadanLab/randomly
A Library for Denoising Single-Cell Data with Random Matrix Theory
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.
HaojiaWu/CellScopes.jl
A Julia package for single cell and spatial data analysis
multitalk/awesome-cell-cell-communication
Collection of computational tools for cell-cell communication inference for single-cell and spatially resolved omics
paulranum11/SPLiT-Seq_demultiplexing
An unofficial demultiplexing strategy for SPLiT-seq RNA-Seq data
caokai1073/Pamona
The software of Pamona, a partial manifold alignment algorithm.
PixelgenTechnologies/pixelator
A command-line tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) assays.
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.
gao-lab/DECIPHER
DECIPHER for learning high-fidelity disentangled embeddings from spatial omics data
Terkild/CITE-seq_optimization
Code and results from TotalSeqC antibody titration and pipeline benchmarking for CITE-seq experiments
tudaga/LabelCorrection
Python code for cross-condition label refinement in single-cell data with HiDDEN
nf-core/pixelator
Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)
yezhenqing/spatial-live
A Lightweight & Versatile Visualization Tool for Spatial-Omics Data
Cajun-data/nanoSPLITS
Github repository for nanoSPLITS manuscript data and R scripts
davismcc/fibroblast-clonality
Website for the fibroblast clonality project conducted at EMBL-EBI and the Wellcome Sanger Institute ca 2017-2019.
TheHumphreysLab/CellScopes.jl
A Julia package for single cell and spatial data analysis
shuzwang/P2_cochlea
It contains the functional code to analyze P2 scRNA-seq and scATAC-seq data.
Catchxu/ACSleuth
Domain Adaptive and Fine-grained Anomaly Detection for Single-cell Sequencing Data and Beyond
deepomicslab/SCOIT
SCOIT is an implementation of a probabilistic tensor decomposition framework for single-cell multi-omics data integration.
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.
aron0093/cy2path
Factorial latent dynamic models trained on Markovian simulations of biological processes using single cell RNA sequencing data.
dn070017/CAVACHON
Cell cluster Analysis with Variational Autoencoder using Conditional Hierarchy Of latent representioN
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.
Flysta3D/multi_omics_atlas
Custom codes for Flysta3D paper.
fungenomics/NB-FOXR2
Analysis for "FOXR2 targets LHX6+/DLX+ neural lineages to drive CNS neuroblastoma" (Jessa*, De Cola*, Chandarana*, et al, Cancer Research, 2024)