aertslab / CREsted
CREsted 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.
☆32Updated this week
Alternatives and similar repositories for CREsted:
Users that are interested in CREsted are comparing it to the libraries listed below
- A method for analyzing scATAC-seq experiments.☆27Updated 2 weeks ago
- Data of genome annotation from full-stack ChromHMM model trained with 1032 datasets from 127 reference epigenomes☆32Updated 8 months ago
- ☆42Updated 4 months ago
- Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace☆39Updated 2 months ago
- ☆27Updated 5 months ago
- pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.☆66Updated last week
- Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…☆58Updated last year
- Individual level Differential Expression Analysis for Single cells☆23Updated 2 years ago
- ☆41Updated this week
- BLADE: Bayesian Log-normAl DEconvolution for enhanced in silico microdissection of bulk gene expression data☆27Updated 11 months ago
- pseudobulking on an AnnData object☆29Updated last week
- Gene regulatory network containing signed transcription factor-target gene interactions☆73Updated 11 months ago
- ☆35Updated 2 weeks ago
- scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics☆52Updated 7 months ago
- ☆16Updated 8 months ago
- Epimap processing and analysis code repository☆33Updated 2 years ago
- Single-cell Iso Prep☆15Updated last year
- ☆29Updated last year
- Estimation of Promoter Activity from RNA-Seq data☆51Updated 3 years ago
- Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens☆41Updated last year
- Functional Inference of Gene Regulation☆41Updated 8 months ago
- Code and analysis pipeline for Smart-seq3 (Hagemann-Jensen et al. 2020).☆51Updated 3 years ago
- ☆26Updated this week
- Single Cell Analysis of Five'Ends☆48Updated last year
- Benchmark of GRNs using the GRETA pipeline☆23Updated this week
- Analysis methods for analysing single cell RNA-seq data; particularly with the goal of checking if tentative clusters of cells are signif…☆37Updated last year
- Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""☆40Updated 2 years ago
- Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks☆28Updated 3 weeks ago
- Preprocesses and Aligns Run-On Sequencing (PRO/GRO/ChRO-seq) data from Single-Read or Paired-End Illumina Sequencing☆26Updated 3 months ago
- ☆30Updated 2 months ago