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    28 repositories

    • medford-vscode

      Public
      The VS Code extension that supports the MEDFORD metadata markup language
      vscodevisual-studio-codevscode-extension
      Python
      •
      MIT License
      •2•1•0•0•Updated Nov 26, 2024Nov 26, 2024

    • medford

      Public
      Human-readible metadata file format to consolidate research information such that it can be stored, updated, and submitted to databases without introducing a huge time investment overhead.
      Python
      •
      MIT License
      •5•9•4•2•Updated Oct 21, 2024Oct 21, 2024

    • RegDiffusion

      Public
      Diffusion model for gene regulatory network inference.
      single-cellgrngene-regulatory-networkdiffusion-models
      Python
      •
      Apache License 2.0
      •4•15•4•0•Updated May 23, 2024May 23, 2024

    • medford-language-server

      Public
      A language server, implementing the Language Server Protocol, for the MEDFORD metadata markup language.
      Python
      •
      MIT License
      •0•3•1•0•Updated Sep 23, 2023Sep 23, 2023

    • Medford-and-Editor-Support-User-Guide

      Public
      TeX
      •0•0•0•0•Updated Aug 13, 2023Aug 13, 2023

    • dazzle

      Public
      Python
      •
      MIT License
      •0•4•0•0•Updated Jun 27, 2023Jun 27, 2023

    • MEDFORD-Spec

      Public
      TeX
      •0•2•1•0•Updated Dec 3, 2022Dec 3, 2022

    • MEDFORD-examples

      Public
      Example MEDFORD metadata files for a variety of datatypes
      MIT License
      •2•1•2•0•Updated Jun 14, 2022Jun 14, 2022

    • pathway-centrality

      Public
      A python program that calculates pathway centrality scores for pathway gene sets based on a given ppi networks
      Python
      •0•0•0•0•Updated Sep 16, 2019Sep 16, 2019

    • Walker

      Public
      Python implementation of Kohler et al.'s random walk with restart
      Python
      •
      MIT License
      •14•29•2•0•Updated Sep 19, 2018Sep 19, 2018

    • detangle-cd

      Public
      Code for Hall-Swan et al. 2017, "Detangling PPI networks to uncover functionally meaningful clusters"
      Python
      •1•1•0•0•Updated Apr 10, 2018Apr 10, 2018

    • semsimcalc

      Public
      Semantic similarity calculation package
      Python
      •1•3•0•0•Updated Apr 24, 2016Apr 24, 2016

    • CANDL_site

      Public
      Python
      •0•0•0•0•Updated Dec 21, 2015Dec 21, 2015

    • dsd-functional

      Public
      Experiments testing ability of DSD to capture functional relationships
      Python
      •0•0•0•0•Updated Nov 6, 2015Nov 6, 2015

    • tools

      Public
      A set of command line programs that interface with the repositories in the TuftsBCB organization.
      Go
      •
      MIT License
      •1•0•0•0•Updated Mar 25, 2014Mar 25, 2014

    • pybcb

      Public
      A small Python module that provides convenience functions for running experiments.
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 25, 2014Mar 25, 2014

    • experiments

      Public
      A collection of experiments used for both exploratory research and in publications.
      Python
      •0•0•0•0•Updated Mar 25, 2014Mar 25, 2014

    • seq

      Public
      Provides common operations for dealing with biological sequence data, including data representation and sequence alignment.
      Go
      •
      MIT License
      •2•1•0•0•Updated Mar 3, 2014Mar 3, 2014

    • fragbag

      Public
      A fast implementation of FragBag for protein structures and sequences.
      Go
      •
      MIT License
      •0•1•0•0•Updated Mar 3, 2014Mar 3, 2014

    • flib

      Public
      A command line tool to interface with fragment libraries.
      Go
      •1•0•0•0•Updated Mar 3, 2014Mar 3, 2014

    • io

      Public
      A set of packages to read and write common file formats produced by computational biology software.
      Go
      •
      MIT License
      •1•10•0•0•Updated Jan 21, 2014Jan 21, 2014

    • apps

      Public
      Library wrappers in Go for computational biology tools that are typically operated from the command line.
      Go
      •
      MIT License
      •0•0•0•0•Updated Dec 19, 2013Dec 19, 2013

    • hhfrag

      Public
      An implementation of Kalev and Habeck's HHfrag algorithm in Go.
      Go
      •
      MIT License
      •0•0•0•0•Updated Dec 19, 2013Dec 19, 2013

    • FunctionalPath

      Public
      Building functional path from Gene Ontology hierarchy and evaluate protein function prediction using the paths
      Java
      •0•0•0•0•Updated Nov 22, 2013Nov 22, 2013

    • foods

      Public
      Our favorite foods.
      0•0•0•0•Updated Oct 25, 2013Oct 25, 2013

    • git-tutorial

      Public
      A git-by-example tutorial that demonstrates basic git commands and pushing to GitHub repositories.
      0•2•0•0•Updated Oct 25, 2013Oct 25, 2013

    • structure

      Public
      A Go library that provides types and functions for common operations on protein structures.
      Go
      •
      MIT License
      •1•0•0•0•Updated Jul 12, 2013Jul 12, 2013

    • SMURFBuild

      Public
      A fork of HMMER-3.0 for the purposes of MRFy and SMURF
      C
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Dec 15, 2011Dec 15, 2011