bioinfomaticsCSU / LoopPredictorView external linksLinks
LoopPredictor: Predicting unknown enhancer-mediated genome topology by an ensemble machine learning model
☆14Jun 18, 2021Updated 4 years ago
Alternatives and similar repositories for LoopPredictor
Users that are interested in LoopPredictor are comparing it to the libraries listed below
Sorting:
- DeepTACT: predicting three-dimensional chromatin contacts via bootstrapping deep learning☆20Jul 23, 2020Updated 5 years ago
- ☆10Oct 24, 2024Updated last year
- Scripts and notebooks used in Akgol Oksuz et al. paper☆11Jan 18, 2021Updated 5 years ago
- Joint normalization of multiple Hi-C matrices, visualization and detection of differential chromatin interactions, supporting covariates.☆10Apr 22, 2022Updated 3 years ago
- Pipeline to implement a "TAD_Pathways" analysis. Discover candidate genes based on association signals in TADs☆11Dec 21, 2019Updated 6 years ago
- General analysis of HiC data, including compartment A/B, domains and loops.☆14Feb 17, 2023Updated 2 years ago
- scGRO-seq analyses codes☆13Jan 9, 2024Updated 2 years ago
- A machine-learning algorithm to predict CTCF-mediated long-range chromatin interactions☆17Nov 7, 2018Updated 7 years ago
- ☆18Sep 6, 2022Updated 3 years ago
- ☆19Jun 8, 2023Updated 2 years ago
- HiCnv is used to call copy number variations and breakpoints from Hi-C data☆23Mar 30, 2024Updated last year
- scripts for analyzing the CVDC data.☆20Dec 5, 2019Updated 6 years ago
- ☆18Mar 12, 2024Updated last year
- A/B compartments for 12 cancer types estimated from TCGA methylation data☆20Jan 18, 2017Updated 9 years ago
- Hi-C Interaction Frequency Inference (HIFI): High-resolution estimation of DNA-DNA interaction frequency from Hi-C data☆24Sep 28, 2022Updated 3 years ago
- Repository containing all code for secondary analysis in the manuscript "On the design of CRISPR-based single cell molecular screens", Hi…☆26Jan 25, 2022Updated 4 years ago
- ☆30Dec 8, 2022Updated 3 years ago
- Scripts for the analysis of TT-seq and DRB/TT-seq data.☆11Mar 11, 2020Updated 5 years ago
- scOpen: single-cell open chromatin analysis via NMF modelling☆28Feb 4, 2023Updated 3 years ago
- Universal Single-Cell Genomics Preprocessing package☆48Feb 2, 2026Updated last week
- Statistically Significant loops from HiChIP data☆46Apr 17, 2024Updated last year
- ATAC-seq processing pipeline☆34Apr 8, 2022Updated 3 years ago
- ☆11Oct 10, 2024Updated last year
- Pipeline to calculate icSHAPE score in genome with sliding window strategy☆12Aug 23, 2022Updated 3 years ago
- Analysis pipeline for processing paired-end Illumina reads obtained after ancient mtDNA target enrichment capture.☆11Mar 27, 2020Updated 5 years ago
- code associated with crane-nature-2015, 10.1038/nature14450☆36Aug 28, 2015Updated 10 years ago
- A neural network framework for predicting the Hi-C chromatin interactions from megabase scale DNA sequence☆33Jan 19, 2026Updated 3 weeks ago
- Localization of transcribed enhancers and quntification of their usage from the initiation sites of bidirectionally transcribed loci☆14Dec 19, 2024Updated last year
- ☆13Sep 14, 2021Updated 4 years ago
- A python port of the Single Molecule Tools software by Adam Wollman, aka. ADEMSCode.☆11Sep 30, 2021Updated 4 years ago
- RIESLING: Super-enhancer identification. (Rapid Identification of EnhancerS LInked to Nearby Genes)☆10Jun 28, 2018Updated 7 years ago
- Computational analyses of WGS, mate-pair, RNA-seq, Hi-C and Capture-C data from highly rearranged balancer chromosomes in Drosophila mela…☆10Sep 25, 2019Updated 6 years ago
- A versatile method for systematic identification of differential RNA splicing across platforms☆15Jan 15, 2026Updated 3 weeks ago
- ☆15May 22, 2025Updated 8 months ago
- ☆12Jan 31, 2023Updated 3 years ago
- Code repository for macsGESTALT single cell lineage tracing analysis https://doi.org/10.1101/2020.08.11.245787☆10May 10, 2021Updated 4 years ago
- Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support☆41Jan 31, 2024Updated 2 years ago
- Statistical analysis for spatial omics data☆11Jul 30, 2022Updated 3 years ago
- Analysis tool for NG-Capture-C, Tri-C and Tiled-C data☆10Oct 13, 2025Updated 4 months ago