masai1116 / SHARE-seq-alignment
pipeline for demultiplex and align both ATAC and RNA data generated in SHARE-seq
☆15Updated 2 years ago
Alternatives and similar repositories for SHARE-seq-alignment:
Users that are interested in SHARE-seq-alignment are comparing it to the libraries listed below
- Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""☆40Updated 2 years ago
- PhyloVelo, Phylogeny-based transcriptomic velocity of single cells☆43Updated last year
- Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.☆61Updated 11 months ago
- Repository to reproduce all analyses for Lareau*, Ludwig*, et al. 2020☆16Updated last year
- ☆13Updated 3 years ago
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆60Updated 10 months ago
- Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity☆26Updated 8 months ago
- Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics☆33Updated this week
- ☆35Updated 7 months ago
- Spatial direct messaging detected by bivariate Moran☆26Updated 3 months ago
- Dissecting the effects of DNA copy number variations on transcriptional programs at single-cell resolution☆12Updated 3 years ago
- Single cell omics biology annotations☆51Updated last month
- An unsupervised approach for the integrative analysis of single-cell multi-omics data☆29Updated 4 years ago
- This repository contains our CellTag workflow, as deployed in our 2018 Biddy et al., Nature paper.☆32Updated 9 months ago
- ☆50Updated 7 months ago
- ☆20Updated last week
- Gene expression deconvolution using dampened weighted least squares☆27Updated 4 years ago
- Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.☆71Updated 3 weeks ago
- Niche Interactions and Cellular Heterogeneity in Extracellular Signaling☆52Updated 6 months ago
- Snakemake pipeline that works with the scIB package to benchmark data integration methods.☆71Updated 2 months ago
- ☆49Updated 6 months ago
- Collection of scripts for analysis of pan fetal immune atlas☆26Updated 2 years ago
- This repository contains all code used for the Human Lung Cell Atlas project.☆49Updated last year
- Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 2022☆53Updated 2 years ago
- Single cell epigenomic clustering based on accessibility pattern☆22Updated 2 years ago
- Co-accessibility network from single-cell ATAC-seq data. Python code, based on Cicero package (R).☆20Updated this week
- pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.☆66Updated last week
- Codebase for PRESCIENT (Potential eneRgy undErlying Single Cell gradIENTs) for generative modeling of single-cell time-series.☆46Updated 2 months ago
- A machine learning method for the discovery of the minimum marker gene combinations for cell type identification from single-cell RNA seq…☆61Updated 2 weeks ago
- ☆26Updated last year