kundajelab / scATAC-reprogLinks
Code for the analysis performed in the paper "Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromatin dynamics during fibroblast reprogramming to pluripotency" by Nair, Ameen et al.
☆12Updated 2 months ago
Alternatives and similar repositories for scATAC-reprog
Users that are interested in scATAC-reprog are comparing it to the libraries listed below
Sorting:
- Parse ArchR arrow files to anndata h5ad☆15Updated 2 years ago
- A method for analyzing scATAC-seq experiments.☆34Updated 6 months ago
- Benchmark of GRNs using the GRETA pipeline☆30Updated this week
- Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace☆41Updated 11 months ago
- ☆37Updated last year
- Neural Crest Fate Decisions☆11Updated 6 years ago
- Inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data☆25Updated 2 years ago
- Quasilinear data representations for single-cell omics data analysis☆43Updated 2 years ago
- Code for Universal Single-Cell Matching with Unpaired Feature Sets☆21Updated 4 years ago
- Gene regulatory network inference for RNA velocity and pseudotime data☆27Updated last month
- A python package for chromVAR☆32Updated 2 years ago
- ☆26Updated 8 months ago
- ☆26Updated 2 years ago
- Code used to analyze single cell RNA and ATAC sequencing in developing human brain☆34Updated 3 years ago
- Functional Inference of Gene Regulation☆49Updated last year
- NATMI: Network Analysis Toolkit for the Multicellular Interactions☆35Updated 4 years ago
- Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""☆40Updated 3 years ago
- Gene regulatory network reconstruction from pseudotemporal single-cell gene expression data☆11Updated last year
- ☆12Updated 2 years ago
- Mitochondrial Alteration Enrichment and Genome Analysis Toolkit☆24Updated last year
- Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-…☆56Updated 6 months ago
- Integrating temporal gene expression modalities for trajectory inference and disease prediction☆10Updated 3 years ago
- Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.☆66Updated 5 months ago
- scOpen: single-cell open chromatin analysis via NMF modelling☆28Updated 2 years ago
- ☆10Updated 3 years ago
- scMEGA: Single-cell Multiomic Enhancer-based Gene regulAtory network inference☆43Updated last year
- Information-based dimensionality reduction☆29Updated last year
- MAGIC - imputation and de-noising single-cell RNA seq data sets☆27Updated 6 years ago
- Learning motif contributions to cell transitions using sequence features and graphs.☆28Updated last year
- Reproducibility code for the manuscript: 'Inferring and perturbing cell fate regulomes in human cerebral organoids☆30Updated 2 years ago