developmental-biology

There are 1 repository under developmental-biology topic.

• Chaste / Chaste

  Chaste - Cancer Heart And Soft Tissue Environment - main public repository.

  mathematical-modellingmathematical-biologycomputational-biologycell-basedelectrophysiologyhpc-applicationsphysiologycancer-researchdevelopmental-biologyc-plus-plus
  Language:C++ 117

• germannp / yalla

  Spheroid models of morphogenesis for the GPU.

  developmental-biologysimulation-frameworkagent-based-modelingmorphogenesisspheroid-modelcenter-dynamics
  Language:Cuda 37

• ComplexOrganizationOfLivingMatter / Epithelia3D

  "Scutoids are a geometrical solution to three-dimensional packing of epithelia" - https://www.nature.com/articles/s41467-018-05376-1.

  computational-biologycomputational-geometrydevelopmental-biologyvoronoiimage-analysis
  Language:MATLAB 11
• 3D-Vertex-Model

  alihashmiii / 3D-Vertex-Model

  vertex model implementation to simulate biological tissue in 3D

  vertex-modelbiophysicsdevelopmental-biologymathematicawolfram-mathematicacomputational-biologycomputational-geometrymathematical-modellingwolfram-languagepolyhedron
  Language:Mathematica 10

• alihashmiii / 2D-vertex-model

  vertex model for simulating two-dimensional epithelial tissues

  biophysicscomputational-biologymathematical-modellingvertex-modelmathematicawolfram-mathematicawolfram-languagedevelopmental-biology
  Language:Mathematica 6

• obophenotype / human-developmental-anatomy-ontology

  Ontology of human developmental anatomy

  obofoundryanatomy-ontologyontologyanatomyhumanmetazoadevelopmental-stagesdevelopmental-biologyuberon
  Language:Makefile 5

• ndalchau / turing-model-reduction

  Matlab scripts to recreate figures of the JR Soc Interface article "Model reduction enables Turing instability analysis of large reaction-diffusion models"

  turingreaction-diffusiondevelopmental-biologymodel-reduction
  Language:MATLAB 4

• vertesy / C.elegans.Spatial.Transcriptomics

  Analysis scripts for the Ebbing et manuscript: "Spatially-resolved transcriptomics in C. elegans identifies sex-specific differences in gene expression patterns"

  developmental-biologyrna-seqspatial-transcriptomicstranscriptomics
  Language:R 4

• hoffmannjordan / Insect-Development-Model

  Python code to model the syncytial development of a cricket in 3D. Additional Mathematica Code for rendering mesh2 objects in povray.

  pythonpovraymathematicadevelopmental-biologynucleusgeometry
  Language:Python 3

• hylasD / tSpace

  single-cell-rna-seqtrajectory-analysissingle-cell-analysiscytofsingle-cellvisualizationdevelopmental-biologycomputational-biologyflow-cytometrytranscriptomicssingle-cell-proteomics
  Language:R 3

• vertesy / X-Reactivation

  Analysis scripts for the Vertesy 2018 paper: "Parental haplotype specific single-cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells"

  scrna-seqepigeneticsallele-specificdevelopmental-biologyhuman-developmenttranscriptomicsimprinting
  Language:R 2

• alihashmiii / cellular-potts-model

  a mathematica implementation of the cellular-potts model

  biophysicsdevelopmental-biologycomputational-biologymathematicawolfram-mathematicawolfram-language
  Language:Mathematica 1

• brickmanlab / proks-salehin-et-al

  Deep Learning Based Models for Preimplantation Mouse and Human Development

  bioinformaticsdevelopmental-biologyscvi-toolsshapley-value
  Language:Jupyter Notebook 1

• bruvellu / terebratalia-wnts

  Expression of Wnt signaling components in the brachiopod Terebratalia transversa

  developmental-biologyevo-devogene-expressionaxial-patterningbrachiopodawnt-signaling
  Language:HTML 1

• ComplexOrganizationOfLivingMatter / Epigraph

  EpiGraph is a Fiji plugin that combines computational geometry and graph theory to measure the degree of arrangement in any computational or natural tessellation.

  imagejfijigraphletspluginbiologytopologydevelopmental-biology
  Language:Java 1

• ComplexOrganizationOfLivingMatter / Fiji-plugins

  GitHub Repository which is used as a Maven Repository

  computational-biologyfiji-pluginfijiimagej-pluginsimagejimage-analysisdevelopmental-biologyepithelia
  1

• Flysta3D / multi_omics_atlas

  Custom codes for Flysta3D paper.

  developmental-biologydrosophila-melanogastersingle-cell-omics
  Language:Python 1

• kaszalab / xenopus-protein-localization

  Analysis of junctional protein localization patterns in epithelial tissues

  computational-biologydevelopmental-biologyimage-processingmicroscopy
  Language:Jupyter Notebook 1

• Mainakdeb / elegant-embryos

  deep-learning for metadata extraction from the C. elegans embryo

  pytorchdata-visualizationdevelopmental-biologyembryogenesisc-elegans
  Language:Jupyter Notebook 1

• Orthogonal-Research-Lab / Periodicity-in-the-Embryo

  developmental-biologytempo-regulationcomputational-biologytheoretical-biologycross-species
  1

• SilasBoyeNissen / Theoretical-tool-bridging-cell-polarities-with-development-of-robust-morphologies

  "Theoretical tool bridging cell polarities with development of robust morphologies" published in eLife (2018)

  organogenesisgastrulationconvergent-extensionmetastable-topologiesmorphogenesistubulogenesisapical-basal-polaritycell-polarityplanar-cell-polaritycell-adhesiontoolboxin-silico-modelorganoid-growthsea-urchinsymmetry-breakingvoronoi-approachbiological-shapesdevelopmental-biologyelifepcp
  Language:MATLAB 1

• airosado / BIOS_FundamentalsClasses-UChicago

  UChicago Molecules to Organisms Fundamentals Sequence R Code: Ecology, Quantitative Bio, Genetics, Physiology, Developmental Bio

  ecologyquantitative-biologygeneticsphysiologydevelopmental-biology
  Language:HTML 0

• antoineruzette / goo_gallery

  Goo is the Blender library for simulating biological cells, tissues and embryos in 3D.

  blenderdevelopmental-biologyrenderingcell-cell-interactionmodeling-and-simulation
  Language:SCSS 0

• asifzubair / BayesianModelSelection

  Bayesian model selection for the Drosophila gap gene network

  bayesian-inferencebayesian-networkdevelopmental-biologymcmc
  Language:Jupyter Notebook 0
• cancerbits.github.io

  cancerbits / cancerbits.github.io

  Lab website.

  cancer-genomicscancerbioinformaticscomputational-biologygenomicsdevelopmental-biologystem-cell-differentiation
  Language:HTML 0

• catohaste / neighbourhood-streak

  Implementation of two models which study how positional information is encoded and interpreted in the developing embryo.

  mathematical-modellingcomputational-modellingdevelopmental-biologypositional-informationmathematical-biologyneighbourhood-watchneighborhood-watchprimitive-streak
  Language:Python 0

• ComplexOrganizationOfLivingMatter / LimeSeg_Pipeline

  "A quantitative principle to understand 3D cellular connectivity in epithelial tubes" Gomez-Galvez et al

  computational-biologycomputational-geometrytissuedevelopmental-biology
  Language:MATLAB 0

• hylasD / MATLAB_version_tSpace

  single-cellcytofsingle-cell-rna-seqsingle-cell-analysistrajectory-analysisvisualizationtranscriptomicssingle-cell-proteomicsflow-cytometrydevelopmental-biologycomputational-biology
  Language:MATLAB 0

• mkondakis / DRIN

  R package that uses rstan capabilities to sample using `HMC' and inference for developmental rate dynamics of species in ecology

  developmental-biologyhmcdevelopment-tools
  Language:R 0

• mragsac / PhD-Dissertation

  Files used to generate Michelle Franc Ragsac's Ph.D. Dissertation

  bioinformaticsdevelopmental-biologyenhancersfunctional-genomicsphd-dissertationphd-thesisnotochord
  Language:TeX 0

• Pegayus / Gene-Expression-Analysis

  Comprehensive analysis of differential gene expression using Bayesian statistics and advanced statistical modeling techniques. The project includes scripts, data, figures, and analysis results.

  bioinformaticsbrain-regionsdata-analysisdevelopmental-biologygene-expressionlinear-modelinglongitudinal-analysisrstatistical-modelingbayesian-modeling
  Language:Jupyter Notebook 0

• nickwawee / MSU_Ad_Hoc_Analyses

  This repo contains code and presentations used for ad-hoc analyses regarding liver cell toxicology and development. It also contains analyses on human and mice immune cells.

  ccadevelopmental-biologyimmune-systemliverpcascrna-seqscrna-seq-analysisseurattoxicologytsne

• Orthogonal-Research-Lab / Developmental-Incongruities-and-Heterochrony

  theoretical-biologydevelopmental-biologyphenotypemorphology-analysisshape-form
  Language:Jupyter Notebook

• sEMTor / sEMTor.github.io

  sEMTor is an online simulation for epithelial-mesenchymal transitions (EMT)

  computational-biologydevelopmental-biologysimulation
  Language:CSS

• YogiOnBioinformatics / ChIP-Seq-Analysis-Nanog-and-H3K27Ac

  Independent project I undertook to perform a full ChIP-Seq analysis of the transcription factor Nanog in Zebrafish embryos.

  computational-genomicsbashlinuxhigh-performance-computingchip-seqdeeptoolshisat2srahistone-modificationsdevelopmental-biologyzebrafishdanio-rerio