single-cell-multiomics

There are 1 repository under single-cell-multiomics topic.

GLUE
gao-lab / GLUE
Graph-linked unified embedding for single-cell multi-omics data integration
bioinformatics deep-learning single-cell single-cell-multiomics
Language:Python 342
pinellolab / dictys
Context specific and dynamic gene regulatory network reconstruction and analysis
dynamic-network gene-regulatory-network network-analysis network-inference network-visualization single-cell-analysis single-cell-multiomics single-cell-network
Language:Python 100
powellgenomicslab / Nebulosa
R package to visualize gene expression data based on weighted kernel density estimation
single-cell single-cell-rna-seq single-cell-analysis single-cell-multiomics
Language:R 64
pyrovelocity
pinellolab / pyrovelocity
𝒫robabilistic modeling of RNA velocity ⬱
cell-fate-determination deep-generative-model developmental-trajectories multiomics probabilistic-models probabilistic-programming pyro rna-splicing rna-splicing-analysis rna-velocity rna-velocity-estimation single-cell-genomics single-cell-multiomics single-cell-rna-seq transcriptomics
Language:Python 35
quadbio / scMultiome_analysis_vignette
Tutorial of single-cell RNA-ATAC multiomic sequencing data analysis
bioinformatics single-cell-analysis single-cell-multiomics tutorial single-cell-atac-seq single-cell-rna-seq
34
sqjin / scAI
An unsupervised approach for the integrative analysis of single-cell multi-omics data
single-cell-multiomics single-cell-multimodal-omics simultaneous-measurements integrative-analysis sparse-epigenomic-profile
Language:R 25
jeongdo801 / scNOVA
scNOVA : Single-Cell Nucleosome Occupancy and genetic Variation Analysis
single-cell-multiomics structural-variation chromatin-accessibiity nucleosome cancer-genomics
Language:R 9
AI4SCR / MatchCLOT
Python package implementing our method MatchCLOT for multimodal single-cell data integration
deep-learning single-cell-analysis single-cell-multiomics
Language:Jupyter Notebook 7
xichensf / magical
R and MATLAB scripts for MAGICAL
non-commercial-license bayesian-inference gene-regulatory-network single-cell-multiomics
Language:R 6
chooliu / snm3Cseq_Pipeline
bioinformatics pipeline for single-nucleus methylation & chromatin conformation capture assay (sn-m3C-seq)
single-cell-hic single-cell-methylation single-cell-multiomics
Language:Jupyter Notebook 0
chooliu / snmCTseq_Pipeline
Luo Lab snmCT-seq bioinformatics pipeline for joint single-nucleus methylation & transcriptome profiles.
single-cell-methylation snmct-seq single-cell-rna-seq smartseq2 single-cell-multiomics
Language:Jupyter Notebook 0
p4rkerw / Wilson_GBio_2024
Containerized workflow for single cell detection of loss of Y chromosome and other mosaic chromosomal alterations in chronic kidney disease
aneuploidy ckd copy-number-variation kidney single-cell single-cell-atac-seq single-cell-genomics single-cell-multiomics single-cell-rna-seq spatial-transcriptomics loss-of-y-chromosome mosaic-chromosomal-alterations somatic-mosaicism
Language:R 0
sagar161286 / multimodal_gdTcells
Multimodal profiling reveals site-specific adaptation and tissue residency hallmarks of γδ T cells across organs in mice.
single-cell-multiomics single-cell-rna-seq t-cells gamma-delta-t-cells
Language:R 0
ytanaka-bio / cisMultiDeep
Workflow to identify functional cis-regulatory regions for each annotated cell type
cis-regulatory-elements cross-species deep-learning enhancers hi-c promoters shap single-cell-atac-seq single-cell-methylation single-cell-multiomics single-cell-rna-seq
Language:Python 0
RuzhangZhao / BenchmarkHVG_old
benchmark single-cell single-cell-genomics single-cell-multiomics single-cell-rna-seq variable-selection highly-variable-gene
Language:R