scverse/rapids_singlecell

rapids_singlecell: GPU-accelerated framework for scRNA analysis

Language: Python - Size: 367 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 235 - Forks: 30

scverse/anndata

Annotated data.

Language: Python - Size: 5.9 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 651 - Forks: 171

scverse/Muon.jl

Muon for Julia

Language: Julia - Size: 1.11 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 27 - Forks: 6

scverse/scanpy

Single-cell analysis in Python. Scales to >100M cells.

Language: Python - Size: 41.1 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 2,174 - Forks: 659

scverse/muon

muon is a multimodal omics Python framework

Language: Python - Size: 5.05 MB - Last synced at: 1 day ago - Pushed at: 24 days ago - Stars: 245 - Forks: 31

lilab-bcb/cirrocumulus

Bring your single-cell data to life

Language: JavaScript - Size: 223 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 88 - Forks: 18

jrs-orellana/xenium2anndata-analysis-workflow

Analysis workflow for 10x Genomics Xenium spatial transcriptomics data. Includes scripts to unpack raw Xenium outputs, convert them into AnnData objects, and perform downstream analyses.

Language: Jupyter Notebook - Size: 178 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 1 - Forks: 0

scverse/anndataR

AnnData interoperability in R

Language: R - Size: 1.49 MB - Last synced at: 9 days ago - Pushed at: 10 days ago - Stars: 102 - Forks: 13

NygenAnalytics/CyteType

Multi-agent driven cell type annotation for single-cell RNA-Seq data stored in Anndata format

Language: Python - Size: 309 KB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 37 - Forks: 9

scverse/mudata

Multimodal Data (.h5mu) implementation for Python

Language: Python - Size: 1.05 MB - Last synced at: 1 day ago - Pushed at: 3 months ago - Stars: 99 - Forks: 20

ArpiarSaundersLab/annsql

The AnnSQL package enables SQL based queries on AnnData objects.

Language: Python - Size: 7.94 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 29 - Forks: 0

theislab/DRVI

Unsupervised Deep Disentangled Representation of Single-Cell Omics

Language: Python - Size: 14 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 48 - Forks: 3

mads-capstone-team24-summer-2025/ghost-cell-busters

This project analyzes single-cell and spatial transcriptomics data from human breast cancers, focusing on distinguishing tumor and normal cell populations through comprehensive computational methods.

Language: Jupyter Notebook - Size: 58.2 MB - Last synced at: 24 days ago - Pushed at: 24 days ago - Stars: 0 - Forks: 0

cantinilab/GRnnData

Awesome GRN enhanced AnnData toolkit

Language: Jupyter Notebook - Size: 16.1 MB - Last synced at: about 8 hours ago - Pushed at: 25 days ago - Stars: 5 - Forks: 2

czbiohub-sf/protdata

Dataloader for common proteomics search engine outputs into AnnData format

Language: Python - Size: 818 KB - Last synced at: 19 days ago - Pushed at: about 2 months ago - Stars: 5 - Forks: 0

complextissue/pytximport

Feature-rich Python implementation of the tximport package for gene count estimation.

Language: Python - Size: 108 MB - Last synced at: 1 day ago - Pushed at: about 1 month ago - Stars: 37 - Forks: 2

czbiohub-sf/grassp

GRaph-based Analysis of Subcellular/Spatial Proteomics

Language: Python - Size: 980 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 0

adabyt/scrnaseq_analysis_project

Single-cell RNA-seq analysis project for learning purposes.

Language: Jupyter Notebook - Size: 16.2 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

PMBio/mudatasets

Multimodal datasets, in MuData format

Language: Python - Size: 66.4 KB - Last synced at: 19 days ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 1

mvinyard/torch-adata

Create PyTorch Datasets from AnnData

Language: Jupyter Notebook - Size: 420 KB - Last synced at: 12 days ago - Pushed at: 6 months ago - Stars: 21 - Forks: 0

YosefLab/treedata

anndata with trees

Language: Python - Size: 1010 KB - Last synced at: 26 days ago - Pushed at: 26 days ago - Stars: 6 - Forks: 3

bnediction/bonesistools

BoNesisTools is a python package proposing bioinformatics tools for upstream and downstream analysis of BoNesis framework

Language: Python - Size: 8.84 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

ilia-kats/MuData

MuData-compatible storage for bioconductor's MultiAssayExperiment

Language: R - Size: 8.58 MB - Last synced at: 2 days ago - Pushed at: 6 months ago - Stars: 6 - Forks: 5

zqfang/toucan

large scale single cell visualization on a desktop PC

Size: 72.5 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

PMBio/MuDataSeurat

.h5mu files interface for Seurat

Language: R - Size: 3.98 MB - Last synced at: 2 days ago - Pushed at: almost 2 years ago - Stars: 32 - Forks: 14

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 at: 3 months ago - Pushed at: over 1 year ago - Stars: 499 - Forks: 105

noamteyssier/adpbulk

pseudobulking on an AnnData object

Language: Python - Size: 21.5 KB - Last synced at: about 1 month ago - Pushed at: 6 months ago - Stars: 32 - Forks: 1

mvinyard/AnnDataQuery

Fetch and format data matrices from AnnData

Language: Python - Size: 457 KB - Last synced at: 18 days ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

srivarra/annsel

A user-friendly library that brings familiar DataFrame-style operations to AnnData objects with a simple and expressive API.

Language: Python - Size: 23.2 MB - Last synced at: 2 days ago - Pushed at: 5 days ago - Stars: 10 - Forks: 1

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: 21 days ago - Pushed at: over 1 year ago - Stars: 11 - Forks: 1

fanglu0411/sgs

SGS, is a user-friendly, collaborative and versatile browser for visualizing single-cell and spatial multiomics data.

Language: JavaScript - Size: 27.3 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 91 - Forks: 19

Iwo-K/genespector

Language: Python - Size: 4.65 MB - Last synced at: 6 days ago - Pushed at: about 3 years ago - Stars: 3 - Forks: 2

lihuax-me/Anndata.jl

Anndata for Julia

Language: Julia - Size: 22.5 KB - Last synced at: 8 days ago - Pushed at: 8 months ago - Stars: 3 - Forks: 0

srivarra/anatomize

Xarray powered Image analysis toolkit.

Language: Python - Size: 111 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

theislab/geome

Language: Python - Size: 20.2 MB - Last synced at: 3 months ago - Pushed at: about 1 year ago - Stars: 16 - Forks: 4

Cai-Lab-at-University-of-Michigan/MiCV

MiCV is a python dash-based web-application that enables researchers to upload raw scRNA-seq data and perform filtering, analysis, and manual annotation.

Language: CSS - Size: 9.3 MB - Last synced at: 9 months ago - Pushed at: over 2 years ago - Stars: 6 - Forks: 0

mvinyard/cell-neighbors

Neighbor graphs for single-cell data (AnnData)

Language: Python - Size: 399 KB - Last synced at: about 2 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

mvinyard/cellplots

Plotting assistant and resources

Language: Python - Size: 320 KB - Last synced at: 6 days ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

mvinyard/cell-ann

Cell approximate nearest neighbors (ANN)

Language: Python - Size: 68.4 KB - Last synced at: 14 days ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

m1ma0314/CSE185Group16_TeeSnee

TeeSnee is an algorithm designed to take high-dimensional gene expression data and represent it in low-dimensional space.

Language: Jupyter Notebook - Size: 1.36 MB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 1

basilkhuder/Seurat-to-RNA-Velocity

A guide to using a Seurat object in conjunction with RNA Velocity

Size: 994 KB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 114 - Forks: 26

mvinyard/annoyance

AnnData-compatible wrapper of Spotify's annoy library.

Language: Python - Size: 16.9 MB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

mvinyard/ann_nmf

AnnData wrapper of the ARD-NMF module from SignatureAnalyzer

Language: Jupyter Notebook - Size: 239 KB - Last synced at: 7 days ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

mvinyard/GTFast

Lift annotations from a GTF file to an adata object.

Language: Python - Size: 48.8 KB - Last synced at: 12 days ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 0

mvinyard/vintools

Michael Vinyard's utilities

Language: Jupyter Notebook - Size: 114 MB - Last synced at: 2 months ago - Pushed at: almost 4 years ago - Stars: 2 - Forks: 1

milescsmith/s2a

Seurat to AnnData conversion

Language: Python - Size: 5.58 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0