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Top 14 single-cell-analysis open source projects

An unofficial demultiplexing strategy for SPLiT-seq RNA-Seq data

✭ 20

python shell scrna-seq single-cell fastq demultiplexing single-cell-rna-seq single-cell-analysis single-cell-omics scrna-seq-analysis single-cell-sequencing split-seq

demuxalot

Reliable, scalable and demultiplexing for single-cell RNA sequencing. Improves genotypes with Expectation-Maximization

✭ 18

python shell scrnaseq demultiplexing biotech single-cell-analysis

CeleScope

Single Cell Analysis Pipelines

✭ 36

python HTML CSS perl r wdl bioinformatics single-cell-analysis

bindSC

Bi-order integration (in silico multi-omics data) of single cell RNA sequencing, single cell ATAC sequencing, spacial transcriptomics and CyTOF data

✭ 24

r integrative-analysis single-cell-analysis

seurat-wrappers

Community-provided extensions to Seurat

✭ 169

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

topometry

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

immunarch

🧬 Immunarch by ImmunoMind: R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires

BEER

BEER: Batch EffEct Remover for single-cell data

✭ 19

r python scrna-seq umap batch-effects single-cell-analysis scatac-seq

SHARP

SHARP: Single-cell RNA-seq Hyper-fast and Accurate processing via ensemble Random Projection

✭ 14

r clustering scrna-seq single-cell-analysis random-projection 1-million-cells

dynmethods

A collection of 50+ trajectory inference methods within a common interface 📥📤

✭ 94

r bioinformatics-algorithms single-cell-rna-seq single-cell-analysis trajectory-inference-methods trajectory-inference pseudotemporal-ordering

DRComparison

Comparison of dimensionality reduction methods

✭ 29

r python shell C++dimensionality-reduction single-cell-analysis

Nebulosa

R package to visualize gene expression data based on weighted kernel density estimation

✭ 50

r single-cell single-cell-rna-seq single-cell-analysis single-cell-multiomics

snATAC

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

✭ 23

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

dyngen

Simulating single-cell data using gene regulatory networks 📠

✭ 59

r Dockerfile benchmarking single-cell single-cell-analysis single-cell-omics

1-14 of 14 single-cell-analysis projects