68 skills found · Page 1 of 3
aertslab / ScenicplusSCENIC+ 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.
pinellolab / ScATAC BenchmarkingBenchmarking computational single cell ATAC-seq methods
crazyhottommy / ScATACseq Analysis Notesmy notes for scATACseq analysis
mdozmorov / ScATAC Seq NotesscATAC-seq data analysis tools and papers
rezakj / ICellRiCellR is an interactive R package designed to facilitate the analysis and visualization of high-throughput single-cell sequencing data. It supports a variety of single-cell technologies, including scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq, and Spatial Transcriptomics (ST).
parashardhapola / ScarfToolkit 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.
fanglu0411 / SgsSGS, is a user-friendly, collaborative and versatile browser for visualizing single-cell and spatial multiomics data.
GreenleafLab / 10x ScATAC 2019Publication Page for Satpathy*, Granja* et al 2019
wbaopaul / ScATAC ProA comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
aertslab / CREstedCREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for designing cell type-specific sequences.
the-ouyang-lab / ShinyCell2ShinyCell2 is a lightweight R package for building interactive, shareable apps to explore single-cell multi-omics, scATAC-seq and spatial transcriptomics data with customizable, publication-ready visualizations.
dbrg77 / Plate ScATAC SeqA rapid and robust plate-based single cell ATAC-seq (scATAC-seq) method
crazyhottommy / ScATACutilsR/Bioconductor package for working with 10x scATACseq data
colomemaria / EpiAneufinderR package to detect breakpoints and assign somies to scATAC-seq data
buenrostrolab / StimATAC Analyses CodeAll code associated with manuscript detailing scATAC and scRNA-seq following stimulus of PBMCs
jmschrei / DragonnfruitA method for analyzing scATAC-seq experiments.
MagpiePKU / EpiTraceCell age determination by scATAC-seq and bulk-ATAC-seq
caleblareau / BapBead-based single-cell atac processing
seasoncloud / AlleloscopeAlleloscope is a method for allele-specific copy number estimation that can be applied to single cell DNA and ATAC sequencing data (separately or in combination). Allele-specific estimation allows for the more accurate delineation of copy number states and the detection of subclonal copy-neutral loss-of-heterozygosity and mirrored CNA events. On scATAC-seq data, Alleloscope allows integrative multi-omic analysis of allele-specific copy number and chromatin accessibility for the same cell.
MiraldiLab / MaxATACTranscription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks
