upendrak

Neural_Network_DNA_Demo

Jupyter Notebook to demonstrate the use of Neural Networks for Transcription Factor Binding Site Prediction

ann-visualizer

A python library for visualizing Artificial Neural Networks (ANN)

icor-codon-optimization

RNN-based Codon Optimization Tool. Publication: https://doi.org/10.1186/s12859-023-05246-8

bioicons

A library of free open source icons for science illustrations in biology and chemistry

lofo-importance

Leave One Feature Out Importance

Codon-optimization

Use machine learning to design codon-optimized DNA sequences for increased protein expression.

GraphBio

GraphBio: a shiny web app to easily perform popular visualization analysis for omics data

Genome-Deep-Learning

DeepExpression

blast-QC

A Quality Control filter and parser for NCBI BLAST XML results.

NN-SVG

Publication-ready NN-architecture schematics.

streamlit-heroku

Dockerizing streamlit application and deploying it on heroku.

ml-pitfalls

Notebooks accompanying the paper "Navigating the pitfalls of applying machine learning in genomics"

jina-video-chat

depthpred

A Deep Learning Model for Predicting Next-Generation Sequencing Depth from DNA Sequence

pseqsid

Calculates pairwise sequence identity, similarity and normalized similarity score of proteins in a multiple sequence alignment.

Graph-Neural-Networks-in-Life-Sciences

scBasset

Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.

graph-kernel-SVM-for-toxicity-of-pesticides-to-bees

reproduce our bee toxicity paper DOI: 10.1063/5.0090573

Data-Science-Interview-Questions-Answers

Curated list of data science interview questions and answers

prefect2-mlops-demo

Demo on how to use Prefect 2 in an ML project

gget

🧬 gget enables efficient querying of genomic reference databases

gretel-synthetics

Synthetic data generators for structured and unstructured text, featuring differentially private learning.

synthetic-data-genomics

Proof of concept code from Gretel.ai and Illumina using generative neural networks to create synthetic versions of mouse genotype and phenotype data.

BRCA-LRseq-pipeline

Pipeline to analyze long-read mRNA isoforms and ORF products sequenced in breast cancer using PacBio Single-Molecule technology.

indaba-pracs-2019

machine-learning-resource

ml-pen-and-paper-exercises

Pen and paper exercises in machine learning

interpret

Fit interpretable models. Explain blackbox machine learning.

OmniXAI

OmniXAI: A Library for eXplainable AI