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Top 28 scrna-seq open source projects

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

clustergrammer2-notebooks

Examples using Clustergrammer2 to explore high-dimensional datasets.

✭ 35

Jupyter Notebook HTML bioinformatics binder jupyter notebook scrna-seq binder-ready

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

✭ 71

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

visium-clustergrammer2

Spatial Transcriptomics Dashboard

✭ 24

Jupyter Notebook python webgl jupyter heatmap scrna-seq voila visium

Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.

Deep learning model for single-cell inference of multi-omic profiles from a single input modality.

✭ 20

Jupyter Notebook python r deep-neural-networks scrna-seq single-cell multi-omics scatac-seq

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

single-cell-papers-with-code

Papers with code for single cell related papers

✭ 20

reproducible-research reproducible-science scrna-seq single-cell single-cell-atac-seq single-cell-omics scrna-seq-analysis paper-with-code

Reconstruction of complex single-cell trajectories using CellRouter

✭ 38

r scrna-seq trajectory-analysis stem-cell-differentiation cell-fate-transitions

Clustering scRNAseq by genotypes

✭ 88

python rust Singularity bioinformatics genomics computational-biology scrna-seq scrnaseq scrna-seq-analysis

Conversion between scRNA-seq objects

✭ 67

r shell conversion bioconductor scrna-seq

Harmony framework for connecting scRNA-seq data from discrete time points

✭ 36

Jupyter Notebook python scrna-seq mnn batch-correction scrna-seq-analysis developmental-trajecotries

Single-cell Hierarchical Poisson Factorization

✭ 52

python dimensionality-reduction scrna-seq variational-bayes

cTPnet Package

✭ 18

python r deep-neural-networks scrna-seq protein-prediction ctp-net surface-protein-imputation

A tool for semi-automatic cell type annotation

✭ 92

python Dockerfile machine-learning scrna-seq single-cell cell-type-classification

BEER: Batch EffEct Remover for single-cell data

✭ 19

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

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.

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

Efficient and precise single-cell reference atlas mapping with Symphony

✭ 69

r C++mapping scrna-seq bioinfo

Demultiplexing pooled scRNA-seq data with or without genotype reference

✭ 34

python scrna-seq variational-inference demultiplex single-cells donor-deconvolution

Spatial alignment of single cell transcriptomic data.

✭ 149

Jupyter Notebook python computational-biology gene-expression scrna-seq spatial-data visium snrna-seq

Single cell type annotation guided by cell atlases, with freedom to be queer

✭ 23

python shell clustering scrna-seq singlecell scrna-seq-analysis cell-atlas leidenalg

scGEAToolbox: Matlab toolbox for single-cell gene expression analyses

✭ 15

HTML matlab workflow scrna-seq analyses rna-seq-analysis tsne matlab-toolbox trajectory dimensionality phate demo-scripts

A tool for fast and accurate summarizing of variant calling format (VCF) files

✭ 55

python TeX genomics mutations scrna-seq variant-calling

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

Imputation method for scRNA-seq based on low-rank approximation

✭ 48

r dropout imputation scrna-seq svd matrix-completion

Discover differential transcript usage from polyA-captured single cell RNA-seq data

✭ 37

r sierra alternative-splicing scrna-seq isoforms alternative-polyadenylation

Clone identification from single-cell data

✭ 49

r scrna-seq single-cell somatic-mutations gibbs-sampling clonal-clustering

1-28 of 28 scrna-seq projects