anndata

There are 0 repository under anndata topic.

scanpy
scverse / scanpy
Single-cell analysis in Python. Scales to >1M cells.
machine-learning data-science visualize-data transcriptomics bioinformatics scanpy anndata python scverse
Language:Python 1875
scverse / anndata
Annotated data.
scanpy data-science transcriptomics bioinformatics machine-learning scverse anndata
Language:Python 569
zhanghao-njmu / SCP
An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
anndata scanpy scatac-seq scrna-pipeline scrna-seq scrna-seq-analysis seurat seurat-objects shiny-app shiny-apps shinyapps single-cell single-cell-analysis single-cell-atac-seq single-cell-genomics single-cell-omics single-cell-pipeline single-cell-rna-seq single-cell-sequencing
Language:R 362
scverse / muon
muon is a multimodal omics Python framework
anndata cite-seq mudata multi-omics multimodal-data multimodal-omics-analysis muon scanpy scatac-seq scrna-seq scverse
Language:Python 210
rapids_singlecell
scverse / rapids_singlecell
Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data processing and analysis.
gpu single-cell anndata bioinformatics scverse
Language:Python 140
basilkhuder / Seurat-to-RNA-Velocity
A guide to using a Seurat object in conjunction with RNA Velocity
seurat integrating-loom kallisto bustools kb-python rna-velocity anndata velocyto scvelo kallisto-bustools
130
fanglu0411 / sgs
SGS, is a user-friendly, collaborative and versatile browser for visualizing single-cell and spatial multiomics data.
anndata mudata sgs spatial-omics zarr visualization genome-browser multimodal scatac sceqtl scrna single-cell schic scmethylc
Language:Dart 127
scverse / mudata
Multimodal Data (.h5mu) implementation for Python
data-analysis genomics multi-omics multimodal-omics-analysis anndata mudata muon scverse
Language:Python 75
lilab-bcb / cirrocumulus
Bring your single-cell data to life
10x anndata bioinformatics data-visualization scanpy scrna-seq seurat single-cell smartseq2 spatial transcriptomics visualization webgl
Language:JavaScript 72
scverse / anndataR
AnnData interoperability in R
anndata h5ad
Language:R 54
scverse / Muon.jl
Muon for Julia
omics multi-omics single-cell muon anndata mudata scverse julia
Language:Julia 26
PMBio / MuDataSeurat
.h5mu files interface for Seurat
seurat multimodal-omics multi-omics scrna-seq anndata mudata
Language:R 25
noamteyssier / adpbulk
pseudobulking on an AnnData object
anndata differential-expression pseudobulk scanpy
Language:Python 23
mvinyard / torch-adata
Create PyTorch Datasets from AnnData
anndata pytorch adata single-cell python
Language:Jupyter Notebook 21
theislab / geome
graph-learning microscopy pytorch-geometric anndata
Language:Python 16
metaspace2020 / metaspace-converter
Download and Convert METASPACE datasets to common formats such as AnnData or SpatialData
anndata metaspace python scverse spatialdata
Language:Python 9
MiCV
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.
gene-expression scanpy pseudotime pseudotime-trajectory marker-genes umap-projection clustering anndata leiden
Language:CSS 6
complextissue / pytximport
Feature-rich Python implementation of the tximport package for gene count estimation.
python rna rna-seq scverse tximport bioinformatics deseq2 anndata
Language:Python 4
ilia-kats / MuData
MuData-compatible storage for bioconductor's MultiAssayExperiment
bioconductor scrna-seq multimodal-omics multi-omics anndata mudata
Language:R 4
PMBio / mudatasets
Multimodal datasets, in MuData format
multimodal-omics multi-omics scrna-seq multiome muon mudata anndata scanpy
Language:Python 3
srivarra / anatomize
Xarray powered Image analysis toolkit.
anndata numba python single-cell-analysis spatial-transcriptomics spatialdata xarray
Language:Python 3
Iwo-K / genespector
scrna-seq anndata scanpy transcriptomics rna-seq
Language:Python 2
mvinyard / GTFast
Lift annotations from a GTF file to an adata object.
genomics gff gtf python gencode anndata single-cell
Language:Python 2
mvinyard / vintools
Michael Vinyard's utilities
single-cell crispr anndata google-cloud bioinformatics genomics python gene-expression chromatin-accessibility
Language:Jupyter Notebook 2
cantinilab / GRnnData
Awesome GRN enhanced AnnData toolkit
anndata gene-regulatory-network rna-seq scverse single-cell utils
Language:Jupyter Notebook 1
milescsmith / s2a
Seurat to AnnData conversion
seurat anndata scanpy
Language:Python 1
mvinyard / ann_nmf
AnnData wrapper of the ARD-NMF module from SignatureAnalyzer
nmf anndata single-cell
Language:Jupyter Notebook 1
mvinyard / annoyance
AnnData-compatible wrapper of Spotify's annoy library.
python approximate-nearest-neighbor-search anndata single-cell cell-type-classifier
Language:Python 1
YosefLab / treedata
anndata with trees
bioinformatics data-science scanpy scverse anndata lineage-tracing
Language:Python 1
m1ma0314 / CSE185Group16_TeeSnee
TeeSnee is an algorithm designed to take high-dimensional gene expression data and represent it in low-dimensional space.
anndata bioinformatics data data-visualization python scanpy srna t-sne
Language:Jupyter Notebook 0
mvinyard / AnnDataQuery
Fetch and format data matrices from AnnData
anndata single-cell
Language:Jupyter Notebook 0
mvinyard / cell-ann
Cell approximate nearest neighbors (ANN)
anndata nearest-neighbors single-cell
Language:Python
mvinyard / cell-neighbors
Neighbor graphs for single-cell data (AnnData)
anndata single-cell neighbor-graphs
Language:Python
mvinyard / cellplots
Plotting assistant and resources
plotting python anndata genomics single-cell
Language:Python