Notebooks accompanying the paper "Navigating the pitfalls of applying machine learning in genomics"
☆46Oct 9, 2023Updated 2 years ago
Alternatives and similar repositories for ml-pitfalls
Users that are interested in ml-pitfalls are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Toolkit for metacell analysis☆24Aug 8, 2024Updated last year
- ☆14Mar 20, 2021Updated 5 years ago
- NEFF Calculator and MSA File Converter☆15May 6, 2026Updated 2 months ago
- Python function for TMB snake plots☆16Feb 12, 2026Updated 5 months ago
- Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of …☆40Mar 27, 2025Updated last year
- 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.
- Code for the analysis performed in the paper "Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromati…☆14Oct 16, 2025Updated 9 months ago
- Chromatin interaction aware gene regulatory modeling with graph attention networks☆29Feb 21, 2023Updated 3 years ago
- HiDeF (Hierarchical community Decoding Framework)☆15Jan 30, 2024Updated 2 years ago
- ENNGene: an Easy Neural Network model building tool for Genomics☆11Mar 31, 2022Updated 4 years ago
- This repository hosts a minimal version of a Python API for BPNet.☆59Jan 24, 2026Updated 5 months ago
- A collection of command-line tools I wrote to make various repetitive tasks more convenient☆16May 17, 2026Updated 2 months ago
- Instructions and analysis scripts for single cell Higher Order Testing (scHOT)☆10Oct 7, 2020Updated 5 years ago
- Integrated Genome Modeling (IGM): multi-modal data-driven simulator of genome structures☆12Jun 15, 2023Updated 3 years ago
- ☆25Aug 20, 2024Updated last year
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Repository for modeling PRO-cap data with the BPNet-like model, ProCapNet.☆21Aug 28, 2025Updated 10 months ago
- ☆27Apr 15, 2025Updated last year
- Kipoi's model zoo API☆243Dec 17, 2025Updated 7 months ago
- Classification of Single cells by Transfer Learning☆11Oct 11, 2025Updated 9 months ago
- BEER: Batch EffEct Remover for single-cell data☆26Jan 9, 2025Updated last year
- ☆16Apr 7, 2026Updated 3 months ago
- In-silico Saturation Mutagenesis implementation with 10x or more speedup for certain architectures.☆23Jun 18, 2022Updated 4 years ago
- Scripts for building computational models of gene regulation with tensorflow☆12Jan 21, 2020Updated 6 years ago
- ☆15Dec 9, 2019Updated 6 years 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.
- HiCnv is used to call copy number variations and breakpoints from Hi-C data☆23Mar 30, 2024Updated 2 years ago
- ☆11Jan 7, 2020Updated 6 years ago
- qtools has helper functions to submit jobs to compute clusters (PBS on TSCC, SGE on oolite) from within Python☆21Sep 20, 2023Updated 2 years ago
- systematic explanation of attribution-based mechanisms for regulatory genomics☆18May 29, 2026Updated last month
- Phenotype detection in pooled genetic perturbation screens☆12Mar 13, 2024Updated 2 years ago
- Slides for my RLadies NYC Presentation☆11Feb 27, 2020Updated 6 years ago
- ChromSCape☆14Jul 30, 2025Updated 11 months ago
- ☆11Apr 4, 2023Updated 3 years ago
- ☆29Nov 7, 2023Updated 2 years ago
- 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.
- ☆33Dec 2, 2022Updated 3 years ago
- Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.☆102Sep 9, 2025Updated 10 months ago
- NGSeminar on the use of Jupyter and R notebooks in biomedical research☆13Jan 28, 2023Updated 3 years ago
- Learning motif contributions to cell transitions using sequence features and graphs.☆27Aug 30, 2024Updated last year
- Software to compute reproducibility and quality scores for Hi-C data☆52Apr 12, 2019Updated 7 years ago
- ☆23May 21, 2026Updated 2 months ago
- Elucidating the Utility of Genomic Elements with Neural Nets☆69Dec 2, 2024Updated last year