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pypdf2

A utility to read and write PDFs with Python

qiaseq-dna

example code for processing reads from QIAGEN QIAseq DNA enrichment kits

r_seq

R scripts for NGS data analysis

rdchiral

Wrapper for RDKit's RunReactants to improve stereochemistry handling

rdkit

The official sources for the RDKit library

resimnet

Implementation of ReSimNet for drug response similarity prediction

rmg-py

Python version of the amazing Reaction Mechanism Generator (RMG).

rnaseqdb

rosettafold

This package contains deep learning models and related scripts for RoseTTAFold

rxnmapper

RXNMapper: Unsupervised attention-guided atom-mapping

sbvs-vina

a framwork for virtual screen via Autodock vina.

schnet

SchNet - a deep learning architecture for quantum chemistry

seqtk

Toolkit for processing sequences in FASTA/Q formats

set2gaussian

code repo for Set2Gaussian

skywalkr

code for Gogleva et al manuscript

skywalkr-graph-features

Example notebooks that illustrate how to generate knowledge-based features. Features can be used in a variety of ML models, including recommender systems.

smi2sdf3d

3D diverse conformers generation using rdkit

sstmap

Solvation Structure and Thermodynamic Mapping

synt-on

Open-source tool for synthons-based library design.

torchmd

End-To-End Molecular Dynamics (MD) Engine using PyTorch

tractability_pipeline_v2

Pipeline for assessing the tractability of potential targets (starting from Gene IDs)

tractaviewer

translate-python

Online translation as a Python module & command line tool. No key, no authentication needed.

trinityrnaseq

Trinity RNA-Seq de novo transcriptome assembly

vcf2maf

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms