62 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.
kundajelab / ChrombpnetBias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
wbaopaul / ScATAC ProA comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
tobiasrausch / ATACseqAnalysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
SUwonglab / PECAPECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
kundajelab / ChromDragoNNCode for the paper "Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts"
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.
rajanil / MsCentipedeA hierarchical multiscale model for inferring transcription factor binding from chromatin accessibility data.
kimmo1019 / DeopenA hybrid deep convolutional neural network for predicting chromatin accessibility
GreenleafLab / ChrAccRAnalyzing chromatin accessibility data in R
MengQiuchen / CPeaksConsensus peaks of chromatin accessibility in the human genome
jsalignon / CactusChromatin ACcessibility and Transcriptomics Unifying Software
RoseYuan / Sc Chromatin BenchmarkReproducible Snakemake workflow for benchmarking single-cell chromatin accessibility analysis methods, published in https://doi.org/10.1186/s13059-024-03356-x
minxueric / Ismb2017 LstmChromatin Accessibility Prediction via Convolutional Long Short-Term Memory Networks with k-mer Embedding
urrutiag / DestinToolkit for single-cell analysis of chromatin accessibility
nf-core / HicarPipeline for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.
brunetlab / CelegansATACseqThe code for Daugherty, et al 2017 - Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans
SUwonglab / TimeRegtime course regulatory analysis from paired gene expression and chromatin accessibility time course data
YosefLab / EpitomePipeline for predicting ChIP-seq peaks in novel cell types using chromatin accessibility
Yin-Shen / CharPlantA de novo prediction tool of chromatin accessible regions for plant genomes
