Deep learning the cis-regulatory code for gene expression in selected model plants
☆25Mar 15, 2024Updated 2 years ago
Alternatives and similar repositories for DeepCRE
Users that are interested in DeepCRE are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆10Jan 27, 2025Updated last year
- A Nextflow pipeline for genome and pan-genome annotation☆16Feb 22, 2026Updated 5 months ago
- Code necessary to reproduce experiments in "FloraBERT: cross-species transfer learning with attention-based neural networks for gene expr…☆13Jul 6, 2022Updated 4 years ago
- PDLLMs: A group of tailored DNA large language models (LLMs) for analyzing plant genomes☆54Jun 5, 2026Updated 2 months ago
- A program to generate a graph which presents a simplified representation of several full length genomes☆13Aug 23, 2018Updated 7 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- ☆16May 21, 2017Updated 9 years ago
- PlantCAD: cross-species modeling of plant genomes☆99Updated this week
- Visualization toolkit for differential splicing events☆21Apr 19, 2026Updated 3 months ago
- Deep learning-based prediction of regulatory genome sequences☆12Apr 20, 2020Updated 6 years ago
- For when you just need a coverage plot.☆11Mar 26, 2021Updated 5 years ago
- Finding patch of conserved amino acid sites in 3D structure☆14Apr 13, 2025Updated last year
- ☆15Jan 18, 2023Updated 3 years ago
- Genotyping lots of samples with big pangenomes☆11Oct 30, 2025Updated 9 months ago
- ☆18Apr 26, 2026Updated 3 months ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- pangenome from maximal blocks in an MSA☆11Sep 17, 2024Updated last year
- Efficient indexing and querying of annotations in a pangenome graph☆10Oct 29, 2025Updated 9 months ago
- convert CHAIN format to PAF format☆15Dec 17, 2024Updated last year
- ENNGene: an Easy Neural Network model building tool for Genomics☆11Mar 31, 2022Updated 4 years ago
- bash script to search for centromeric repeat patterns in PacBio data, using several current tools (trf and R)☆13Dec 1, 2016Updated 9 years ago
- Shared k-mer content between two genomes☆18Jun 21, 2023Updated 3 years ago
- Training materials for all things bioinformatics☆17Jun 29, 2026Updated last month
- Haplotype-aware assembly of complex regions and small genomes☆15Aug 2, 2026Updated last week
- A plant organellar Graphical Fragment Assembly toolkit☆16Sep 10, 2025Updated 11 months ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Web based viewer for small to medium GFA format files, similar to Bandage☆13Jun 19, 2026Updated last month
- snpless-nf - A Nextflow pipeline for time-course analysis with bacterial NGS whole-genome data.☆14May 12, 2024Updated 2 years ago
- Syllabus: MUSA 620 - Data Wrangling and Data Visualization☆10May 12, 2017Updated 9 years ago
- Fast, self-contained VCF to MAF converter with embedded annotation (Rust rewrite of vcf2maf)☆18Jun 23, 2026Updated last month
- Enumerating bubbles in pangenome graphs☆15Updated this week
- Single cell ANANSE Gene-regulatory-network analysis from Seurat objects☆11Nov 12, 2023Updated 2 years ago
- ☆25Mar 27, 2026Updated 4 months ago
- ☆22Sep 22, 2022Updated 3 years ago
- Methylation analysis pipeline for genome graph☆16May 25, 2025Updated last year
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Codes for the lettuce resequencing project in 2020☆31Jun 28, 2021Updated 5 years ago
- ☆15Jun 29, 2021Updated 5 years ago
- This tutorial is a guide to perform TWAS with the data used in Torres‐Rodríguez, J. Vladimir, et al. "Population‐level gene expression ca…☆26Feb 23, 2026Updated 5 months ago
- The genome annotation service provides automated gene annotation based on the RAST system. This deploys both client and service component…☆11Sep 22, 2020Updated 5 years ago
- ☆43Jan 19, 2024Updated 2 years ago
- Monorepo for Apollo 3 server-side and client-side (JBrowse 2 plugin) components.☆16Updated this week
- Rust implementation of Flavia95's GFAtoVCF☆16Jan 17, 2022Updated 4 years ago