Stochastic Sequence Propagation - A Keras Model for optimizing DNA, RNA and protein sequences based on a predictor
☆50Aug 13, 2024Updated last year
Alternatives and similar repositories for seqprop
Users that are interested in seqprop are comparing it to the libraries listed below
Sorting:
- Deep Exploration Networks - Diverse Deep Generative Models for DNA, RNA and Protein Sequences☆31Oct 1, 2021Updated 4 years ago
- Code for "Optimizing 5’UTRs for mRNA-delivered gene editing using deep learning"☆24Jul 2, 2024Updated last year
- APA Regression Net - Predict and Engineer Alternative Polyadenylation☆40Oct 1, 2021Updated 4 years ago
- Modeling of human 5′ UTRs enables the design of new sequences for target levels of translation and 5′ UTR variant prediction.☆58Jul 3, 2019Updated 6 years ago
- The C. elegans transcriptome at single cell resolution☆11Mar 28, 2018Updated 7 years ago
- Interpretation by Deep Generative Masking for Biological Sequences☆37Dec 9, 2021Updated 4 years ago
- Python wrapper for MaxEntScan to calculate splice site strength.☆17Jul 8, 2022Updated 3 years ago
- Deep learning based prediction of pi-helices in protein sequences☆11Mar 24, 2023Updated 2 years ago
- A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.☆87Sep 24, 2025Updated 5 months ago
- ☆19Mar 21, 2024Updated last year
- The standalone version of SPOT-1D-Single available for public use for research purposes.☆24May 19, 2024Updated last year
- A python library for creating simulated regulatory DNA sequences☆39Feb 22, 2023Updated 3 years ago
- Prediction of RNA modifications and their stoichiometry from per-read features: current intensity, dwell time and trace (Begik*, Lucas* e…☆24Dec 21, 2022Updated 3 years ago
- Python implementation of TEISER also capable of using SHAPE structural probing data☆12Jan 7, 2025Updated last year
- Tool for finding matches to degenerate sequence motifs in FASTA files.☆13Mar 11, 2024Updated last year
- Multivariate Gaussian Direct Coupling Analysis for residue contact prediction in protein families - Julia module☆22Jan 27, 2022Updated 4 years ago
- Code accompanying the paper "Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively…☆12Aug 26, 2021Updated 4 years ago
- Use Thor's Axe to cut exons into their evolutionary building blocks☆12Feb 3, 2026Updated last month
- Direct RNA publication scripts☆11Sep 20, 2017Updated 8 years ago
- Saluki, a method to predict mRNA half-lives from sequence☆27Oct 7, 2022Updated 3 years ago
- ☆27Apr 15, 2025Updated 10 months ago
- Tissue-specific variant effect predictions on splicing☆42May 23, 2023Updated 2 years ago
- Scripts and data deposition for de novo heterodimers manuscript☆11Dec 15, 2018Updated 7 years ago
- Code for the Framepool model☆14Feb 1, 2025Updated last year
- HiCOPS: Computational framework for peptide identification from MS data through accelerated database search☆10Mar 24, 2023Updated 2 years ago
- Normalization and difference calling for Next Generation Sequencing (NGS) data via joint multinomial modeling.☆11Oct 8, 2021Updated 4 years ago
- Code for the paper "Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellula…☆44Jun 9, 2021Updated 4 years ago
- TF MOtif Discovery from Importance SCOres☆167Feb 20, 2026Updated last week
- Ledidi turns any machine learning model into a biological sequence editor, allowing you to design sequences with desired properties.☆101Jan 31, 2026Updated last month
- Analysis steps to calculate RNA Velocity in Bulk RNA-Seq samples. Step by Step Guide.☆17Jan 7, 2020Updated 6 years ago
- We present Envision, an accurate predictor of protein variant molecular effect, trained using large-scale experimental mutagenesis data. …☆19Jan 5, 2018Updated 8 years ago
- Scripts for building computational models of gene regulation with tensorflow☆11Jan 21, 2020Updated 6 years ago
- A Christmas tree protein☆19Dec 27, 2024Updated last year
- Faster, more accurate and entirely open source method for predicting contacts in proteins☆12May 21, 2018Updated 7 years ago
- ProtT5 (Transformer) embeddings used for residue wise disorder prediction in proteins☆11Mar 11, 2024Updated last year
- A package for making MuE observation models in Edward2.☆13Jun 10, 2021Updated 4 years ago
- Code for 5UTR project☆26May 20, 2023Updated 2 years ago
- Boltzmann machine learning for Potts models of biological data☆12Jul 24, 2024Updated last year
- Interpretable genotype-phenotype landscape modeling☆36Dec 3, 2023Updated 2 years ago