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Top 32 single-cell-rna-seq open source projects

Signac

✭ 15

r single-cell-rna-seq seurat cellular-phenotypes

tGPLVM: A Nonparametric, Generative Model for Manifold Learning with scRNA-seq experimental data

✭ 16

python dimensionality-reduction manifold-learing single-cell-rna-seq manifold-learning-algorithms

SPLiT-Seq demultiplexing

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

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

✭ 34

Jupyter Notebook python shell machine-learning bioinformatics rna-seq computational-biology ontologies cell-type-classification single-cell-rna-seq cell-biology cell-type

No description or website provided.

✭ 170

r single-cell-rna-seq

Pipeline for initial analysis of droplet-based single-cell RNA-seq data

✭ 71

C++r CMake pipeline scrna-seq preprocessing single-cell-rna-seq

Stacked Denoising AutoEncoder based on TensorFlow

✭ 23

python r bioinformatics deep-neural-networks tensorflow autoencoders single-cell-rna-seq

kmer-homology-paper

Manuscript for functional prediction of transcriptomic “dark matter” across species

✭ 12

HTML shell TeX evolution single-cell single-cell-rna-seq cross-species comparative-transcriptomes

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

✭ 30

r Dockerfile TeX transcriptomics single-cell deconvolution single-cell-rna-seq

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

✭ 78

rust shell rna-seq quantification transcriptomics single-cell 10x single-cell-rna-seq

An R implementation of the SINCERA pipeline for single cell RNA-seq profiling analysis

✭ 20

r signature driving single-cell-rna-seq celltype

Discrete Distributional Differential Expression

✭ 19

python differential-expression single-cell-rna-seq human-cell-atlas

Metacell - Single-cell mRNA Analysis

✭ 63

r single-cell-rna-seq

OrchestratingSingleCellAnalysis-release

An online companion to the OSCA manuscript demonstrating Bioconductor resources and workflows for single-cell RNA-seq analysis.

✭ 35

rna-seq book single-cell single-cell-rna-seq book-release

scLearn：Learning for single cell assignment

✭ 26

r assignment metric-learning single-cell-rna-seq

Single-cell exploratory data analysis for RNA-Seq

✭ 33

python clustering-algorithm single-cell-rna-seq

scisorseqr is an R-package for processing of single-cell long read data and analyzing differential isoform expression across any two conditions

✭ 21

r shell awk python splicing-quantification differential-analysis single-cell-rna-seq long-read-sequencing

Single-cell Orientation Tracing

✭ 20

r python single-cell-rna-seq

Differential expression analysis for single-cell RNA-seq data.

✭ 137

python bioinformatics tensorflow transcriptomics gene-set-enrichment differential-expression single-cell-rna-seq

Code for the empty droplet and cell detection project from the HCA Hackathon.

✭ 16

TeX r simulations manuscript single-cell-rna-seq human-cell-atlas

Processing of single cell RNAseq data for the recovery of TCRs in python

✭ 22

python perl rna-seq single-cell-rna-seq

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.

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

scRNAseq cell cluster labeling

Scripts to run and benchmark scRNA-seq cell cluster labeling methods

✭ 41

perl r Raku benchmark datasets single-cell-rna-seq cell-clusters labeling-methods

A R framework for pipeline benchmarking, with application to single-cell RNAseq

✭ 38

r benchmark clustering pipelines bioconductor single-cell-rna-seq pipeline-benchmarking

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

Deep Learning based cell composition analysis with Scaden.

✭ 61

python Dockerfile machine-learning bioinformatics rna-seq deep-learning deconvolution single-cell-rna-seq cell-composition-analysis

All-in-one analysis pipeline

✭ 28

haskell transcriptional-regulatory-network single-cell-rna-seq rna-seq-pipeline single-cell-atac-seq atac-seq-pipeline

arshamg-scrnaseq-wgan

Wasserstein Generative Adversarial Network for analysing scRNAseq data

✭ 33

python r deep-learning tensorflow generative-adversarial-network gan single-cell-rna-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 Bayesian model for compositional single-cell data analysis

✭ 109

Jupyter Notebook python tensorflow statistical-analysis single-cell-rna-seq compositional-changes

1-32 of 32 single-cell-rna-seq projects