Starred repositories
Compute generation probabilities of CDR3 amino acid and nucleotide sequences
R package that allows for visualization of the KNN of an embedding compared to the KNN of the original high-dimensional data.
Biomni: a general-purpose biomedical AI agent
Tools to clean, transform, merge and reshape data
iFeature is a comprehensive Python-based toolkit for generating various numerical feature representation schemes from protein or peptide sequences. iFeature is capable of calculating and extracting…
TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data
BraCeR - reconstruction of B cell receptor sequences from single-cell RNAseq data
The aim of this project is to determine a suitable conventional machine learning model using the ChEMBL dataset to predict bioactivity values of different compounds on a SARS-coronavirus replicase …
Prediction using Logistic Regression with 87% accuracy
SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
📝 [Paper/Tutorial] T-cell repertoire annotation and motif discovery
In-silico method written in Python and R to determine HLA genotypes of a sample. seq2HLA takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising all HLA allel…
⚙️ Matching T-cell repertoire against a database of TCR antigen specificities
Amino Acid Embedding Representation as Machine Learning Features
Using k-mers to call HLA alleles in RNA sequencing data
Mol2vec notebooks for use with Binder service
Material for lecture at the EMBL Single Cell Course 2016
iLearnPlus is the first machine-learning platform with both graphical- and web-based user interface that enables the construction of automated machine-learning pipelines for computational analysis …
The code in this repository is from my master thesis. This project aims to automatically segment carotid from 3D MR brain image, and use the segmented carotid to extract Time-Activity-Curve from PE…
Mol2vec - an unsupervised machine learning approach to learn vector representations of molecular substructures
Clinically Reportable TCR repertoires