Topic: computational-biology Goto Github

👇 Here are 910 public repositories matching this topic...

3dmol / 3dmol.js
computational-biology,WebGL accelerated JavaScript molecular graphics library
Organization: 3dmol
molecular-graphics molecular-modeling computational-biology computational-chemistry

a-r-j / graphein
computational-biology,Protein Graph Library
User: a-r-j
Home Page: https://graphein.ai/
protein protein-structure deep-learning pytorch graph-neural-networks dgl computational-biology bioinformatics structural-biology protein-data-bank protein-design geometric-deep-learning pytorch-geometric python interactomics interactome rna ppi-networks gene-regulatory-networks drug-discovery

angelruizmoreno / jupyter_dock
computational-biology,Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.
User: angelruizmoreno
molecular-docking autodock autodock-vina ledock mdanalysis rdkit openbabel cheminformatics computational-biology jupyter-notebook

aquaskyline / clairvoyante
computational-biology,Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
User: aquaskyline
variant-calling deep-learning bioinformatics computational-biology

aquaskyline / soapdenovo2
computational-biology,Next generation sequencing reads de novo assembler.
User: aquaskyline
bioinformatics assembly soapdenovo genome computational-biology

asoplata / open-computational-neuroscience-resources
computational-biology,A publicly-editable collection of open computational neuroscience resources
User: asoplata
neuroscience neuroscience-data neural-simulators neuroimaging-data electrophysiological-data neuroscience-methods computational-neuroscience computational-biology awesome awesome-list

bebop / poly
computational-biology,A Go package for engineering organisms.
Organization: bebop
Home Page: https://pkg.go.dev/github.com/bebop/poly
synthetic-biology synbio genetic-engineering molecular-biology bioengineering computational-biology bioinformatics dna fasta genbank

benjamin-lee / deep-rules
computational-biology,Ten Quick Tips for Deep Learning in Biology
User: benjamin-lee
Home Page: https://benjamin-lee.github.io/deep-rules/
deep-learning manuscript manubot biology bioinformatics computational-biology machine-learning data-science genomics

biopandas / biopandas
computational-biology,Working with molecular structures in pandas DataFrames
Organization: biopandas
Home Page: https://BioPandas.github.io/biopandas/
molecular-structures pandas-dataframe pdb mol2 protein-structure molecules pdb-files drug-discovery computational-biology bioinformatics

biosyntax / biosyntax
computational-biology,Syntax highlighting for computational biology
Organization: biosyntax
Home Page: http://bioSyntax.org
bam bioinformatics computational-biology fasta gedit less pdb sublime-text syntax-highlighting vcf vim

biotite-dev / biotite
computational-biology,A comprehensive library for computational molecular biology
Organization: biotite-dev
Home Page: https://www.biotite-python.org
bioinformatics computational-biology structural-biology sequence-analysis pdb-files

blengerich / compbiodatasetsformachinelearning
computational-biology,A Curated List of Computational Biology Datasets Suitable for Machine Learning
User: blengerich
datasets curated-list machine-learning computational-biology dataset computational-biology-datasets biomedical-data-science

broadinstitute / tangram
computational-biology,Spatial alignment of single cell transcriptomic data.
Organization: broadinstitute
spatial-data visium gene-expression scrna-seq snrna-seq computational-biology

burkesquires / python_biologist
computational-biology,Python Programming for Biologists
User: burkesquires
python biology biology-education bioinformatics computational-biology data-analysis data-science

camurban / pterasoftware
computational-biology,Ptera Software is a fast, easy-to-use, and open-source software package for analyzing flapping-wing flight.
User: camurban
unmanned-aerial-vehicle ornithopter ornithology aerospace aerodynamics aerospace-engineering aeronautics computational-biology computational-fluid-dynamics vortex-lattice-method

chanzuckerberg / czid-web
computational-biology,Infectious Disease Sequencing Platform
Organization: chanzuckerberg
Home Page: https://czid.org/
infectious-diseases genomics sequencing metagenomic science next-generation-sequencing research biology virology bioinformatics

chaste / chaste
computational-biology,Chaste - Cancer Heart And Soft Tissue Environment - main public repository.
Organization: chaste
Home Page: https://chaste.github.io/
mathematical-modelling mathematical-biology computational-biology cell-based electrophysiology hpc-applications physiology cancer-research developmental-biology c-plus-plus

coleygroup / pyscreener
computational-biology,pythonic interface to virtual screening software
Organization: coleygroup
virtual-screening computational-biology molecular-docking distributed-computing ray

developer-y / cs-video-courses
computational-biology,List of Computer Science courses with video lectures.
User: developer-y
computer-science algorithms systems databases machine-learning web-development security computer-architecture bioinformatics robotics

eselkin / awesome-computational-neuroscience
computational-biology,A list of schools and researchers in computational neuroscience
User: eselkin
awesome awesome-list computational computational-biology computational-linguistics computational-neuroscience computational-psychiatry computational-psychology mathematical-neuroscience neuroscience

fbrundu / pymrmr
computational-biology,Python3 binding to mRMR Feature Selection algorithm (currently not maintained)
User: fbrundu
feature-selection computational-biology data-science mutual-information gene-expression

franciscozorrilla / metagem
computational-biology,:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
User: franciscozorrilla
Home Page: https://franciscozorrilla.github.io/metaGEM/
metagenomics computational-biology metabolic-models gut-microbiome snakemake metagenome-assembled-genomes mags metabolism bioinformatics flux-balance-analysis

gcorso / diffdock
computational-biology,Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
User: gcorso
Home Page: https://arxiv.org/abs/2210.01776
diffusion-models docking binding computational-biology equivariance machine-learning non-euclidean-geometry score-based-models

hku-bal / clair
computational-biology,Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling
Organization: hku-bal
variant-calling deep-learning bioinformatics computational-biology

hku-bal / clair3
computational-biology,Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
Organization: hku-bal
deep-learning variant-calling computational-biology nanopore long-reads genomics ont-data ont-models illumina pacbio variant-detection

jisungk / riddle
computational-biology,Race and ethnicity Imputation from Disease history with Deep LEarning
User: jisungk
Home Page: https://riddle.ai
deep-learning machine-learning neural-networks imputation epidemiology computational-biology bioinformatics biology

jonathanking / protein-transformer
computational-biology,Predicting protein structure through sequence modeling
User: jonathanking
protein-structure sequence-to-sequence attention computational-biology machine-learning structural-biology

ketatam / diffdock-pp
computational-biology,Implementation of DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models in PyTorch (ICLR 2023 - MLDD Workshop)
User: ketatam
Home Page: https://arxiv.org/abs/2304.03889
computational-biology diffusion-models machine-learning protein-docking

mariewelt / openchem
computational-biology,OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research
User: mariewelt
Home Page: https://mariewelt.github.io/OpenChem/
computational-chemistry computational-biology deep-learning deep-neural-networks graph-convolutional-networks drug-discovery drug-design qsar predictive-modeling machine-learning

markovmodel / deeptime
computational-biology,Deep learning meets molecular dynamics.
Organization: markovmodel
pytorch tensorflow dimension-reduction markov-model data-analysis machine-learning autoencoder time-series computational-biology computational-chemistry

michellab / biosimspace
computational-biology,Code and resources for the EPSRC BioSimSpace project.
Organization: michellab
Home Page: https://biosimspace.org
biomolecular-simulation interoperability ccpbiosim computational-chemistry computational-physics computational-biology molecular-dynamics reproducibility reproducible-research

minkaixu / geodiff
computational-biology,Implementation of GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation (ICLR 2022).
User: minkaixu
molecule graph-neural-networks generative-models conformation iclr iclr2022 diffusion-models score-matching computational-biology computational-chemistry

mrzresearcharena / pyfeat
computational-biology,A Python-based Effective Feature Generation Tool from DNA, RNA, and Protein Sequences
User: mrzresearcharena
Home Page: http://rafsanjani.pythonanywhere.com/
computational-biology bioinformatics genomics proteomics

msmbuilder / vde
computational-biology,Variational Autoencoder for Dimensionality Reduction of Time-Series
Organization: msmbuilder
variational-autoencoder molecular-dynamics computational-chemistry computational-biology time-series deep-learning pytorch python

omicsml / dance
computational-biology,DANCE: a deep learning library and benchmark platform for single-cell analysis
Organization: omicsml
Home Page: https://pydance.readthedocs.io
bioinformatics dance data-science deep-learning graph-neural-networks machine-learning multimodality python single-cell spatial-transcriptomics

opencobra / cobrapy
computational-biology,COBRApy is a package for constraint-based modeling of metabolic networks.
Organization: opencobra
Home Page: http://opencobra.github.io/cobrapy/
modeling metabolic-models metabolic-network metabolism flux bioinformatics biochemistry computational-biology systems-biology cell-design

opensim-org / opensim-core
computational-biology,SimTK OpenSim C++ libraries and command-line applications, and Java/Python wrapping.
Organization: opensim-org
Home Page: https://opensim.stanford.edu
science simulation biological-simulations biomechanics engineering computational-science computational-biology musculoskeletal-models

phonchi / computational-cryoem
computational-biology,A curated list of awesome computational cryo-EM methods.
User: phonchi
cryo-em electron-microscopy single-particle-analisys computational-biology structural-biology cryoem

plotly / dash-cytoscape
computational-biology,Interactive network visualization in Python and Dash, powered by Cytoscape.js
Organization: plotly
Home Page: https://dash.plot.ly/cytoscape
plotly-dash plotly dash cytoscape cytoscapejs network-visualization network-graph graph-theory bioinformatics computational-biology

pnpnpn / dna2vec
computational-biology,dna2vec: Consistent vector representations of variable-length k-mers
User: pnpnpn
bioinformatics computational-biology embeddings machine-learning ml neural-network nlp python word-embeddings word2vec

qizhipei / fabind
computational-biology,FABind: Fast and Accurate Protein-Ligand Binding (NeurIPS 2023)
User: qizhipei
Home Page: https://arxiv.org/abs/2310.06763
binding bioinformatics computational-biology docking machine-learning

samsinai / flexs
computational-biology,Fitness landscape exploration sandbox for biological sequence design.
User: samsinai
Home Page: https://flexs.readthedocs.io/en/latest/index.html
machine-learning benchmarking protein-design deep-learning deep-reinforcement-learning computational-biology bayesian-optimization

scikit-bio / scikit-bio
computational-biology,scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.
Organization: scikit-bio
Home Page: https://scikit.bio
bioinformatics computational-biology

seq-lang / seq
computational-biology,A high-performance, Pythonic language for bioinformatics
Organization: seq-lang
Home Page: https://seq-lang.org
bioinformatics computational-biology genomics programming-language domain-specific-language compiler python

sorgerlab / indra
computational-biology,INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.
Organization: sorgerlab
Home Page: http://indra.bio
systems-biology modeling biology computational-biology bioinformatics pysb nlp indra sbml

swsoyee / r3dmol
computational-biology,🧬 An R package for visualizing molecular data in 3D
User: swsoyee
Home Page: https://swsoyee.github.io/r3dmol/
protein protein-structure 3d r htmlwidgets visualization molecular-graphics molecular-modeling computational-biology computational-chemistry

theochem / iodata
computational-biology,Python library for reading, writing, and converting computational chemistry file formats and generating input files.
Organization: theochem
Home Page: https://iodata.readthedocs.io/en/latest/index.html
quantum-chemistry quantum-chemistry-programs quantum-chemistry-packages computational-chemistry computational-biology computational-physics file-format-converter data-parsing json-schema theoretical-chemistry

ucscgenomebrowser / kent
computational-biology,UCSC Genome Browser source tree. Stable branch: "beta".
Organization: ucscgenomebrowser
Home Page: http://genome.ucsc.edu/
genomics-visualization data-visualisation bioinformatics computational-biology

wheaton5 / souporcell
computational-biology,Clustering scRNAseq by genotypes
User: wheaton5
scrna-seq scrnaseq scrna-seq-analysis bioinformatics computational-biology genomics

yoseflab / cassiopeia
computational-biology,A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction
Organization: yoseflab
Home Page: https://cassiopeia-lineage.readthedocs.io/en/latest/
single-cell-rna-seq lineage-tracing single-cell-lineage-tracing computational-phylogenetics computational-biology crispr-cas9