Repository Index

DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

• kmer
• dnabert-model
• kmer-format
• gpu

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.

• deep-learning
• protein-sequences
• protein-structure
• semi-supervised-learning

Official release of the ProGen models

• language-model
• protein
• generative-model

Generation of protein sequences and evolutionary alignments via discrete diffusion models

• discrete-diffusion
• generative-model
• multiple-sequence-alignment
• protein-sequences

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

• variant-calling
• genomics
• vcf-manipulation
• genotyping

OmegaFold Release Code

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

• sequence-alignment
• edit-distance
• levehnstein-distance
• library

Spatial Single Cell Analysis in Python

• single-cell-rna-seq
• single-cell-genomics
• spatial-transcriptomics
• spatial-analysis

Generative biopolymer design with rich conditioning.

A Python Package for Protein Dynamics Analysis

• python
• protein
• dynamics

A tool for semi-automatic cell type classification

• python
• single-cell
• machine-learning
• scrna-seq

RNA Velocity generalized through dynamical modeling

The repository host gives no description.

Graph-linked unified embedding for single-cell multi-omics data integration

• bioinformatics
• deep-learning
• single-cell
• single-cell-multiomics

Sequential regulatory activity predictions with deep convolutional neural networks.

A dependency-free cross-platform swiss army knife for PDB files.

• python
• protein
• pdb
• bioinformatics

Benchmarking analysis of data integration tools

The repository host gives no description.

GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations

Reference mapping for single-cell genomics

• single-cell
• deep-learning
• rna-seq-analysis
• data-integration

Genomic Pretrained Network - GPN, GPN-MSA, PhyloGPN, GPN-Star

• dna
• language-model
• variant-effect-prediction
• genomics

The repository host gives no description.

UCE is a zero-shot foundation model for single-cell gene expression data

The repository host gives no description.