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global-chemA Chemical Knowledge Graph of What is Common in the World.
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graphkit-learnA python package for graph kernels, graph edit distances, and graph pre-image problem.
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mol frameChemical Structure Handling for Pandas DataFrames
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Hap.pyHaplotype VCF comparison tools
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TeamTeriGenomics using open source tools, running on GCP or AWS
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CanvasxpressJavaScript VisualizationTools
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BiopythonOfficial git repository for Biopython (originally converted from CVS)
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fastapi-redisShowcase of Redis integration with Python FastAPI framework as API backend for RDKit: Open-Source Cheminformatics Software
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Scaff10XPipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads
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sample-sheetA permissively licensed library designed to replace Illumina's Experiment Manager
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ACPCChemoinformatics tool for ligand-based virtual screening
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Cyvcf2cython + htslib == fast VCF and BCF processing
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pysmilesA lightweight python-only library for reading and writing SMILES strings
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Single Cell PseudotimeAn overview of algorithms for estimating pseudotime in single-cell RNA-seq data
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Homebrew Bio🍺🔬 Bioinformatics formulae for the Homebrew package manager (macOS and Linux)
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PrimerMinerR mased batch sequence downloader, with primer development and in silico evaluation capabilities
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graphchemGraph-based machine learning for chemical property prediction
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Hh SuiteRemote protein homology detection suite.
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CANDOComputational Analysis of Novel Drug Opportunities
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BridgeDbThe BridgeDb Library source code
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molecular-VAEImplementation of the paper - Automatic chemical design using a data-driven continuous representation of molecules
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ensembl-comparaThe Ensembl Compara Perl API and SQL schema
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GRAFIMOGRAph-based Finding of Individual Motif Occurrences
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jgi-queryA simple command-line tool to download data from Joint Genome Institute databases
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BowtieAn ultrafast memory-efficient short read aligner
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SnifflesStructural variation caller using third generation sequencing
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gnparserGNparser normalises scientific names and extracts their semantic elements.
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Dash.jlDash for Julia - A Julia interface to the Dash ecosystem for creating analytic web applications in Julia. No JavaScript required.
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molassemblerChemoinformatics toolkit with support for inorganic molecules
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siriusSIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)
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xyz2graphConvert an xyz file into a molecular graph and create a 3D visualisation of the graph.
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MiniasmUltrafast de novo assembly for long noisy reads (though having no consensus step)
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ScopyAn integrated negative design python library for desirable HTS/VS database design
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StrelkaStrelka2 germline and somatic small variant caller
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unimapA EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment
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SourmashQuickly search, compare, and analyze genomic and metagenomic data sets.
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GLaDOSWeb Interface for ChEMBL @ EMBL-EBI
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dysgudysgu-SV is a collection of tools for calling structural variants using short or long reads
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DashAnalytical Web Apps for Python, R, Julia, and Jupyter. No JavaScript Required.
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chemicaliteAn SQLite extension for chemoinformatics applications.
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Abyss🔬 Assemble large genomes using short reads
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wgs2ncbiToolkit for preparing genomes for submission to NCBI
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rkmhClassify sequencing reads using MinHash.
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CeleScopeSingle Cell Analysis Pipelines
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protwisProtwis is the backbone of the GPCRdb. The GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs).
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PHATPathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform
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