GGboy-Zzz

Pinned Repositories

scenicplus
SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
Language:Jupyter Notebook192 10 35332
ABC-Enhancer-Gene-Prediction
Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
Language:Python00
cellranger
10XscRNAseq preprocess
Language:Shell0 1 00
GSEApy
Gene Set Enrichment Analysis in Python
Language:Python00
ROGUE
Assessing the purity of single cell population
Language:R00
scATAC-reprog
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.
Language:Jupyter Notebook0 0 00
ss3xpress-data-analysis
pipeline for analysis ss3xpress data
Language:Shell0 1 00
chrombpnet
Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
Language:Jupyter Notebook127 40 13534
scvi-tools
Deep probabilistic analysis of single-cell and spatial omics data
Language:Python1.3k 26 1k366
zUMIs
zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
Language:R275 13 38768

GGboy-Zzz's Repositories

GGboy-Zzz/cellranger
10XscRNAseq preprocess
Language:Shell0 1 00
GGboy-Zzz/scATAC-reprog
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.
Language:Jupyter Notebook0 0 00
GGboy-Zzz/ss3xpress-data-analysis
pipeline for analysis ss3xpress data
Language:Shell0 1 00