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Top 10 single-cell-genomics open source projects

Reference mapping for single-cell genomics

✭ 175

Jupyter Notebook python deep-learning scrna-seq data-integration single-cell rna-seq-analysis single-cell-genomics batch-correction multimodal-deep-learning multiomics human-cell-atlas

seurat-wrappers

Community-provided extensions to Seurat

✭ 169

r shell community single-cell-genomics single-cell-analysis

single cell portal

Tutorials, workflows, and convenience scripts for Single Cell Portal

✭ 41

HTML python wdl r Jupyter Notebook Dockerfile rna-seq-analysis single-cell-genomics human-cell-atlas

A comprehensive dimensional reduction framework to recover the latent topology from high-dimensional data.

✭ 64

python visualization data-science machine-learning clustering graphs scikit-learn data-visualization information-visualization dimensionality-reduction topology-visualiztion dimension-reduction topological-data-analysis knowledge-representation topology-optimization single-cell-genomics single-cell-analysis single-cell-omics data-topology

Spatial Single Cell Analysis in Python

✭ 235

python shell data-visualization spatial-analysis image-analysis single-cell-genomics single-cell-rna-seq spatial-transcriptomics squidpy

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

Cloud-based single-cell copy-number variation analysis tool

✭ 42

PHP javascript r shell C++CSS bioinformatics sequencing single-cell-genomics

<<------ Use SnapATAC!!

✭ 23

python shell c clustering bioinformatics-pipeline single-cell-genomics single-cell-analysis single-cell-atac-seq

CellRank for directed single-cell fate mapping

✭ 222

python shell data-science machine-learning bioinformatics genetics trajectory-generation markov-chains manifold-learning single-cell-genomics single-cell-rna-seq cell-fate-transitions fuzzy-clustering-analyses rna-velocity cell-fate-determination

A deep learning-based tool for alignment and integration of single cell genomic data across multiple datasets, species, conditions, batches

✭ 32

r scrna-seq single-cell single-cell-genomics scrna-seq-analysis human-cell-atlas

1-10 of 10 single-cell-genomics projects