GitHub topics: scverse
scverse/scvi-tools
Deep probabilistic analysis of single-cell and spatial omics data
Language: Python - Size: 148 MB - Last synced at: about 9 hours ago - Pushed at: 2 days ago - Stars: 1,368 - Forks: 387
scverse/scanpy
Single-cell analysis in Python. Scales to >100M cells.
Language: Python - Size: 40.9 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 2,074 - Forks: 626
nf-core/scdownstream
A single cell transcriptomics pipeline for QC, integration and making the data presentable
Language: Nextflow - Size: 2.08 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 54 - Forks: 23
scverse/pertpy
Perturbation Analysis in the scverse ecosystem.
Language: Python - Size: 98.3 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 170 - Forks: 29
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: 366 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 191 - Forks: 26
scverse/anndata
Annotated data.
Language: Python - Size: 5.59 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 617 - Forks: 163
scverse/scvi-tutorials
Notebooks used in scvi-tools tutorials
Language: Jupyter Notebook - Size: 669 MB - Last synced at: 6 days ago - Pushed at: 7 days ago - Stars: 52 - Forks: 28
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: 79.4 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 37 - Forks: 6
complextissue/spatiomic
A Python package for unsupervised analysis of spatial (prote)omics data.
Language: Python - Size: 60.9 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 2 - Forks: 0
complextissue/pyclustree
A Python alternative to `clustree` for assessing single-cell RNA-sequencing clusters.
Language: Python - Size: 3.7 MB - Last synced at: 14 days ago - Pushed at: 15 days ago - Stars: 5 - Forks: 0
scverse/muon
muon is a multimodal omics Python framework
Language: Python - Size: 5.05 MB - Last synced at: 13 days ago - Pushed at: about 2 months ago - Stars: 231 - Forks: 31
scverse/mudata
Multimodal Data (.h5mu) implementation for Python
Language: Python - Size: 1.05 MB - Last synced at: 15 days ago - Pushed at: about 1 month ago - Stars: 92 - Forks: 19
theislab/ehrapy
Electronic Health Record Analysis with Python.
Language: Python - Size: 175 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 283 - Forks: 24
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: 12 days ago - Pushed at: 12 days ago - Stars: 150 - Forks: 28
YosefLab/treedata
anndata with trees
Language: Python - Size: 614 KB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 3 - Forks: 3
YosefLab/pycea
scverse lineage tracing analysis toolkit
Language: Python - Size: 601 KB - Last synced at: 24 days ago - Pushed at: 24 days ago - Stars: 0 - Forks: 1
complextissue/pytximport
Feature-rich Python implementation of the tximport package for gene count estimation.
Language: Python - Size: 108 MB - Last synced at: 15 days ago - Pushed at: about 1 month ago - Stars: 35 - Forks: 2
scverse/Muon.jl
Muon for Julia
Language: Julia - Size: 1.05 MB - Last synced at: 14 days ago - Pushed at: about 2 months ago - Stars: 28 - Forks: 6
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 18 hours ago - Pushed at: about 2 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: 25 days 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: about 2 months ago - Pushed at: about 2 months ago - Stars: 13 - Forks: 7
scverse/governance
Governance docs for scverse
Size: 136 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 7 - Forks: 0
cantinilab/GRnnData
Awesome GRN enhanced AnnData toolkit
Language: Jupyter Notebook - Size: 16.1 MB - Last synced at: 6 days ago - Pushed at: 3 months ago - Stars: 3 - Forks: 2
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: 7 months ago - Pushed at: 7 months ago - Stars: 1 - Forks: 0
daisybio/scanalysis
A single cell transcriptomics pipeline for QC, integration and making the data presentable
Language: Nextflow - Size: 676 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0
vjcitn/scviR
experimental interface between R and scvi-tools
Language: R - Size: 24.4 MB - Last synced at: 12 months ago - Pushed at: about 1 year 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
gtca/chame
Chromatin accessibility module
Language: Python - Size: 1.65 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 0
