Ecosyste.ms: Repos
An open API service providing repository metadata for many open source software ecosystems.
GitHub topics: single-cell-omics
prabhakarlab/Banksy
BANKSY: spatial clustering
Language: R - Size: 595 MB - Last synced: 5 days ago - Pushed: 6 days ago - Stars: 49 - Forks: 11
TheHumphreysLab/CellScopes.jl Fork of HaojiaWu/CellScopes.jl
A Julia package for single cell and spatial data analysis
Language: Julia - Size: 126 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 5 - Forks: 1
HaojiaWu/CellScopes.jl
A Julia package for single cell and spatial data analysis
Language: Julia - Size: 126 MB - Last synced: 1 day ago - Pushed: 11 days ago - Stars: 19 - Forks: 2
saeyslab/nichenetr
NicheNet: predict active ligand-target links between interacting cells
Language: R - Size: 151 MB - Last synced: 12 days ago - Pushed: 13 days ago - Stars: 441 - Forks: 113
dynverse/dyngen
Simulating single-cell data using gene regulatory networks 📠
Language: HTML - Size: 607 MB - Last synced: 14 days ago - Pushed: 4 months ago - Stars: 68 - Forks: 6
nf-core/pixelator
Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)
Language: Nextflow - Size: 4.04 MB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 6 - Forks: 3
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: Python - Size: 25.7 MB - Last synced: 21 days ago - Pushed: 21 days ago - Stars: 30 - Forks: 1
SuhasSrinivasan/multiplexed-scrna
Multiplexed droplet scRNA-seq Kang et al Nat Biotechnol 2018
Language: HTML - Size: 8.87 MB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 0 - Forks: 0
neurogenomics/MAGMA_Celltyping
Find causal cell-types underlying complex trait genetics
Language: R - Size: 245 MB - Last synced: 26 days ago - Pushed: 26 days ago - Stars: 66 - Forks: 29
multitalk/awesome-cell-cell-communication
Collection of computational tools for cell-cell communication inference for single-cell and spatially resolved omics
Language: Jupyter Notebook - Size: 17.6 MB - Last synced: 21 days ago - Pushed: 3 months ago - Stars: 21 - Forks: 4
bschilder/thesis
PhD thesis written in Quarto.
Language: HTML - Size: 605 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0
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: Python - Size: 761 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0
saezlab/ccc_protocols
LIANA x Tensor-cell2cell Protocols
Language: Jupyter Notebook - Size: 168 MB - Last synced: 26 days ago - Pushed: about 1 month ago - Stars: 1 - Forks: 3
PixelgenTechnologies/pixelator
A command-line tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) assays.
Language: Python - Size: 36 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 9 - Forks: 1
caokai1073/Pamona
The software of Pamona, a partial manifold alignment algorithm.
Language: Jupyter Notebook - Size: 41.4 MB - Last synced: 15 days ago - Pushed: about 3 years ago - Stars: 19 - Forks: 3
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++ - Size: 957 KB - Last synced: about 2 months ago - Pushed: about 3 years ago - Stars: 43 - Forks: 15
yezhenqing/spatial-live
A Lightweight & Versatile Visualization Tool for Spatial-Omics Data
Language: TypeScript - Size: 233 MB - Last synced: about 2 months ago - Pushed: 6 months ago - Stars: 7 - Forks: 0
dynverse/dynverse
A set of tools supporting the development, execution, and benchmarking of trajectory inference methods. 🌍
Language: R - Size: 566 KB - Last synced: 21 days ago - Pushed: about 3 years ago - Stars: 71 - Forks: 17
antosalerno/TEPA_code
Analysing single-cell and DSP data to test the effect of copper chelation with TEPA in Neuroblastoma mice
Language: R - Size: 648 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0
zhanghao-njmu/SCP
An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
Language: R - Size: 788 MB - Last synced: 3 months ago - Pushed: 4 months ago - Stars: 284 - Forks: 54
RabadanLab/randomly
A Library for Denoising Single-Cell Data with Random Matrix Theory
Language: Jupyter Notebook - Size: 4.52 MB - Last synced: 3 months ago - Pushed: 10 months ago - Stars: 36 - Forks: 15
th789/vitessce-shiny
R Shiny app for Vitessce, an integrative and interactive data visualization tool for exploration of spatial single-cell experiments.
Language: R - Size: 27.9 MB - Last synced: 4 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0
ToureLaminelab/RNAvelocity
RNA velocity is a high-dimensional vector that predicts the future state of individual cells on a timescale of hours.
Language: Jupyter Notebook - Size: 43.8 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 1 - Forks: 0
xmc811/Scillus
R Package for Single-Cell Dataset Processing and Visualization
Language: R - Size: 11.1 MB - Last synced: 3 months ago - Pushed: almost 3 years ago - Stars: 46 - Forks: 9
Flysta3D/multi_omics_atlas
Custom codes for Flysta3D paper.
Language: Python - Size: 88.9 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 1 - Forks: 0
Cajun-data/nanoSPLITS
Github repository for nanoSPLITS manuscript data and R scripts
Language: HTML - Size: 377 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 3 - Forks: 0
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: Python - Size: 2.17 MB - Last synced: 6 months ago - Pushed: over 2 years ago - Stars: 2 - Forks: 0
dn070017/CAVACHON
Cell cluster Analysis with Variational Autoencoder using Conditional Hierarchy Of latent representioN
Language: Python - Size: 776 KB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0
genecell/single-cell-papers-with-code
Papers with code for single cell related papers
Size: 44.9 KB - Last synced: 7 months ago - Pushed: 11 months ago - Stars: 225 - Forks: 47
paulranum11/SPLiT-Seq_demultiplexing
An unofficial demultiplexing strategy for SPLiT-seq RNA-Seq data
Language: Python - Size: 6.83 MB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 25 - Forks: 9
dynverse/dyno
Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕
Language: R - Size: 114 MB - Last synced: 7 months ago - Pushed: almost 3 years ago - Stars: 149 - Forks: 32
tudaga/LabelCorrection
Python code for cross-condition label refinement in single-cell data with HiDDEN
Language: Jupyter Notebook - Size: 728 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 1
vjcitn/BiocPyInterop
Material for Bioconductor 2023 workshop on interoperation with python
Language: R - Size: 296 KB - Last synced: about 1 month ago - Pushed: 11 months ago - Stars: 0 - Forks: 1
Terkild/CITE-seq_optimization
Code and results from TotalSeqC antibody titration and pipeline benchmarking for CITE-seq experiments
Language: R - Size: 210 MB - Last synced: 8 months ago - Pushed: about 3 years ago - Stars: 9 - Forks: 2
fanzhanglab/AtRiskRA_CyTOF
Source code for the At-Risk RA work
Language: Jupyter Notebook - Size: 79.5 MB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 1 - Forks: 1
aron0093/cy2path
Factorial latent dynamic models trained on Markovian simulations of biological processes using single cell RNA sequencing data.
Language: Python - Size: 182 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 1 - Forks: 0
Harsheen98/Single-Cell-Omics-Projects
Repository for projects in Single Cell
Language: R - Size: 794 KB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0
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 Notebook - Size: 7.45 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 8 - Forks: 3
Griffan/popscle
(NOTE:This is development fork, please refer to official repo at statgen:https://github.com/statgen/popscle) Freemuxlet methods and auxilary tools
Language: C++ - Size: 258 KB - Last synced: 11 months ago - Pushed: over 4 years ago - Stars: 1 - Forks: 0
agniRS/COVID-severity-classification-using-sc-RNA-seq-data
As part of the IEE Healthcare Summit Data Hackathon(2022) Challenge designed a classification model to predict severity of COVID-19 infection from scRNA-seq data.
Language: Python - Size: 280 KB - Last synced: 3 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0
poloarol/single-cell-transcriptomics-app
A R Shiny App for single-cell analysis
Language: R - Size: 14.2 MB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0
poloarol/poloarol
Computational Biologist and Machine Learning Enthusiast
Size: 12.7 KB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0
poloarol/awesome-computational-biochemistry
Papers and Tools that would guide your journey in Computational Biochemistry
Size: 18.6 KB - Last synced: 22 days ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0
fanzhanglab/TteK
Code for Jonsson*, Zhang*, et al, TteK (Granzyme K+ CD8 T cells), Science Translational Medicine, 2022: the core population of inflamed human tissue-associated CD8 T cells.
Language: Jupyter Notebook - Size: 9.49 MB - Last synced: over 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0
shuzwang/P2_cochlea
It contains the functional code to analyze P2 scRNA-seq and scATAC-seq data.
Language: R - Size: 162 KB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 5 - Forks: 0
davismcc/fibroblast-clonality
Website for the fibroblast clonality project conducted at EMBL-EBI and the Wellcome Sanger Institute ca 2017-2019.
Language: R - Size: 94.8 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 5 - Forks: 3
rahulbhadani/scomix
Single-Cell Data Science
Language: Python - Size: 99.6 KB - Last synced: 10 days ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0
