anndata
There are 38 repositories under anndata topic.
scverse/scanpy
Single-cell analysis in Python. Scales to >1M cells.
scverse/anndata
Annotated data.
zhanghao-njmu/SCP
An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
scverse/muon
muon is a multimodal omics Python framework
scverse/rapids_singlecell
Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data processing and analysis.
basilkhuder/Seurat-to-RNA-Velocity
A guide to using a Seurat object in conjunction with RNA Velocity
fanglu0411/sgs
SGS, is a user-friendly, collaborative and versatile browser for visualizing single-cell and spatial multiomics data.
scverse/mudata
Multimodal Data (.h5mu) implementation for Python
lilab-bcb/cirrocumulus
Bring your single-cell data to life
scverse/anndataR
AnnData interoperability in R
theislab/DRVI
Unsupervised Deep Disentangled Representation of Single-Cell Omics
complextissue/pytximport
Feature-rich Python implementation of the tximport package for gene count estimation.
noamteyssier/adpbulk
pseudobulking on an AnnData object
scverse/Muon.jl
Muon for Julia
PMBio/MuDataSeurat
.h5mu files interface for Seurat
mvinyard/torch-adata
Create PyTorch Datasets from AnnData
metaspace2020/metaspace-converter
Download and Convert METASPACE datasets to common formats such as AnnData or SpatialData
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.
ArpiarSaundersLab/annsql
The AnnSQL package enables SQL based queries on AnnData objects.
ilia-kats/MuData
MuData-compatible storage for bioconductor's MultiAssayExperiment
srivarra/annsel
An AnnData accessor powered by Narwhals to perform DataFrame-style selection, filtering and indexing operations on AnnData Objects.
cantinilab/GRnnData
Awesome GRN enhanced AnnData toolkit
srivarra/anatomize
Xarray powered multidimensional-image analysis toolkit.
mvinyard/GTFast
Lift annotations from a GTF file to an adata object.
mvinyard/vintools
Michael Vinyard's utilities
PMBio/mudatasets
Multimodal datasets, in MuData format
YosefLab/treedata
anndata with trees
zehua0417/Anndata.jl
Anndata for Julia
milescsmith/s2a
Seurat to AnnData conversion
mvinyard/ann_nmf
AnnData wrapper of the ARD-NMF module from SignatureAnalyzer
mvinyard/annoyance
AnnData-compatible wrapper of Spotify's annoy library.
mvinyard/cell-ann
Cell approximate nearest neighbors (ANN)
mvinyard/cell-neighbors
Neighbor graphs for single-cell data (AnnData)
mvinyard/cellplots
Plotting assistant and resources