GitHub topics: scverse
complextissue/spatiomic
A Python package for unsupervised analysis of spatial (prote)omics data.
Language: Python - Size: 60.9 MB - Last synced at: about 15 hours ago - Pushed at: about 16 hours ago - Stars: 2 - Forks: 0
YosefLab/treedata
anndata with trees
Language: Python - Size: 615 KB - Last synced at: about 18 hours ago - Pushed at: about 19 hours ago - Stars: 5 - Forks: 3
scverse/scvi-tools
Deep probabilistic analysis of single-cell and spatial omics data
Language: Python - Size: 144 MB - Last synced at: 2 days ago - Pushed at: 3 days ago - Stars: 1,386 - Forks: 390
nf-core/scdownstream
A single cell transcriptomics pipeline for QC, integration and making the data presentable
Language: Nextflow - Size: 2.23 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 66 - Forks: 29
scverse/anndata
Annotated data.
Language: Python - Size: 5.86 MB - Last synced at: 2 days ago - Pushed at: 3 days ago - Stars: 627 - Forks: 164
cantinilab/GRnnData
Awesome GRN enhanced AnnData toolkit
Language: Jupyter Notebook - Size: 16.1 MB - Last synced at: about 11 hours ago - Pushed at: 4 days ago - Stars: 4 - Forks: 2
scverse/scvi-tutorials
Notebooks used in scvi-tools tutorials
Language: Jupyter Notebook - Size: 755 MB - Last synced at: 3 days ago - Pushed at: 4 days ago - Stars: 52 - Forks: 28
scverse/rapids_singlecell
Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data processing and analysis.
Language: Python - Size: 367 MB - Last synced at: 4 days ago - Pushed at: 5 days ago - Stars: 208 - Forks: 26
scverse/pertpy
Perturbation Analysis in the scverse ecosystem.
Language: Python - Size: 98.2 MB - Last synced at: 4 days ago - Pushed at: 5 days ago - Stars: 177 - Forks: 30
scverse/scanpy
Single-cell analysis in Python. Scales to >100M cells.
Language: Python - Size: 40.9 MB - Last synced at: 6 days ago - Pushed at: 10 days ago - Stars: 2,102 - Forks: 638
complextissue/pytximport
Feature-rich Python implementation of the tximport package for gene count estimation.
Language: Python - Size: 108 MB - Last synced at: 3 days ago - Pushed at: 10 days ago - Stars: 36 - Forks: 2
scverse/muon
muon is a multimodal omics Python framework
Language: Python - Size: 5.05 MB - Last synced at: 5 days ago - Pushed at: 3 months ago - Stars: 236 - Forks: 31
scverse/mudata
Multimodal Data (.h5mu) implementation for Python
Language: Python - Size: 1.05 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 98 - Forks: 19
aertslab/CREsted
CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for designing cell type-specific sequences.
Language: Python - Size: 90.9 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 39 - Forks: 6
theislab/ehrapy
Electronic Health Record Analysis with Python.
Language: Python - Size: 175 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 292 - Forks: 25
icbi-lab/infercnvpy
Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
Language: Python - Size: 36.7 MB - Last synced at: 8 days ago - Pushed at: 12 days ago - Stars: 156 - Forks: 28
scverse/Muon.jl
Muon for Julia
Language: Julia - Size: 1.05 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 28 - Forks: 6
complextissue/pyclustree
A Python alternative to `clustree` for assessing single-cell RNA-sequencing clusters.
Language: Python - Size: 4.5 MB - Last synced at: 6 days ago - Pushed at: 7 days ago - Stars: 6 - Forks: 0
gtca/chame
Chromatin analysis module
Language: Python - Size: 1.65 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 4 - Forks: 0
YosefLab/pycea
scverse lineage tracing analysis toolkit
Language: Python - Size: 601 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 1
TileDB-Inc/scverse-ml-workshop-2024
Scripts/Notebooks for "Training models on atlas-scale single-cell datasets" at scverse Conference 2024
Language: Jupyter Notebook - Size: 9.4 MB - Last synced at: about 3 hours ago - Pushed at: 3 months ago - Stars: 8 - Forks: 0
metaspace2020/metaspace-converter
Download and Convert METASPACE datasets to common formats such as AnnData or SpatialData
Language: Python - Size: 4.35 MB - Last synced at: about 20 hours ago - Pushed at: about 1 year ago - Stars: 11 - Forks: 1
scverse/muon-tutorials
Tutorials for multimodal omics data analysis
Language: Jupyter Notebook - Size: 17.7 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 13 - Forks: 7
scverse/governance
Governance docs for scverse
Size: 136 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 7 - Forks: 0
hds-sandbox/scverse-2024-workshop
Dimensionality reduction and interactive web visualization for the scverse 2024 conference
Language: Jupyter Notebook - Size: 80.3 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 1 - Forks: 0
vjcitn/scviR
experimental interface between R and scvi-tools
Language: R - Size: 24.5 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 6 - Forks: 0
scverse/muon-site
Muon website
Language: JavaScript - Size: 514 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0