Deep learning the cis-regulatory code for gene expression in selected model plants
☆28Mar 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:
- A tool for pangenome graph-based phased diploid genome inference.☆10Sep 19, 2026Updated last month
- ☆12Jul 24, 2026Updated 3 months ago
- online variation graph induction☆12Oct 21, 2025Updated last year
- PDLLMs: A group of tailored DNA large language models (LLMs) for analyzing plant genomes☆57Sep 5, 2026Updated last month
- ☆10Jan 27, 2025Updated last year
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- ☆15May 3, 2023Updated 3 years ago
- Utilities to manipulate pangenome collections using multi-MUMs☆20Sep 16, 2026Updated last month
- AlfaPang builds pangenome graphs without alignments or references.☆17Oct 16, 2026Updated 2 weeks ago
- KaryoScope: rapid, alignment-free sequence annotation for the pangenome era☆29Oct 21, 2026Updated last week
- ☆25Sep 22, 2026Updated last month
- ☆12May 23, 2024Updated 2 years ago
- ☆14Jul 1, 2025Updated last year
- 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
- A Nextflow pipeline for genome and pan-genome annotation☆17Feb 22, 2026Updated 8 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.
- Scripts used to perform analyses in Rice et al. (2023)☆16Dec 28, 2023Updated 2 years ago
- Haplotype-aware assembly of complex regions and small genomes☆15Oct 12, 2026Updated 2 weeks ago
- Code for assembly approach presented in "Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspri…☆15Nov 20, 2023Updated 2 years ago
- Detailed bioinformatics scripts and methods used in the Maize-Pan-genome paper.☆17Oct 8, 2025Updated last year
- ☆16May 21, 2017Updated 9 years ago
- PlantCAD: cross-species modeling of plant genomes☆106Aug 7, 2026Updated 2 months ago
- Visualization toolkit for differential splicing events☆21Apr 19, 2026Updated 6 months ago
- A program to generate a graph which presents a simplified representation of several full length genomes☆13Aug 23, 2018Updated 8 years ago
- ☆12Updated this week
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Unzip assembly graphs with Hi-C data and/or long reads.☆29May 7, 2026Updated 5 months ago
- Deep learning-based prediction of regulatory genome sequences☆12Apr 20, 2020Updated 6 years ago
- ☆18Apr 26, 2026Updated 6 months ago
- A Python library for manipulation of CIGAR, MSA, and other alignment formats.☆12Apr 14, 2026Updated 6 months ago
- A newly designed version of Bamsnap with Long Read Support (LRS) which inspired by bamsnap (https://github.com/parklab/bamsnap)☆14Oct 13, 2026Updated 2 weeks ago
- ☆15Jan 18, 2023Updated 3 years ago
- We developed GenomeSyn as a new tool for constructing and visualizing genome synteny, its novel design and implementation can serve as a …☆36Jan 3, 2022Updated 4 years ago
- base-level dotplots from PAF alignments☆36Updated this week
- ☆53Jun 27, 2026Updated 4 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.
- PlantGeneAnn: Plant Gene Annotator☆14Oct 19, 2026Updated last week
- ☆19Aug 6, 2025Updated last year
- OIST Bioinfo user group☆13Oct 23, 2026Updated last week
- ☆32Oct 7, 2026Updated 3 weeks ago
- Genotyping lots of samples with big pangenomes☆11Oct 30, 2025Updated last year
- For when you just need a coverage plot.☆11Mar 26, 2021Updated 5 years ago
- Rapid alignment-free method for introgression screening and GWAS using k-mer profiles☆32Apr 22, 2026Updated 6 months ago