Pinned Repositories
dazzle
git-tutorial
A git-by-example tutorial that demonstrates basic git commands and pushing to GitHub repositories.
io
A set of packages to read and write common file formats produced by computational biology software.
medford
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.
medford-language-server
A language server, implementing the Language Server Protocol, for the MEDFORD metadata markup language.
MEDFORD-Spec
RegDiffusion
Diffusion model for gene regulatory network inference.
semsimcalc
Semantic similarity calculation package
seq
Provides common operations for dealing with biological sequence data, including data representation and sequence alignment.
Walker
Python implementation of Kohler et al.'s random walk with restart
Tufts Bioinformatics and Computational Biology Research Group's Repositories
TuftsBCB/Walker
Python implementation of Kohler et al.'s random walk with restart
TuftsBCB/io
A set of packages to read and write common file formats produced by computational biology software.
TuftsBCB/medford
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.
TuftsBCB/RegDiffusion
Diffusion model for gene regulatory network inference.
TuftsBCB/dazzle
TuftsBCB/medford-language-server
A language server, implementing the Language Server Protocol, for the MEDFORD metadata markup language.
TuftsBCB/semsimcalc
Semantic similarity calculation package
TuftsBCB/git-tutorial
A git-by-example tutorial that demonstrates basic git commands and pushing to GitHub repositories.
TuftsBCB/MEDFORD-Spec
TuftsBCB/detangle-cd
Code for Hall-Swan et al. 2017, "Detangling PPI networks to uncover functionally meaningful clusters"
TuftsBCB/fragbag
A fast implementation of FragBag for protein structures and sequences.
TuftsBCB/MEDFORD-examples
Example MEDFORD metadata files for a variety of datatypes
TuftsBCB/medford-vscode
The VS Code extension that supports the MEDFORD metadata markup language
TuftsBCB/seq
Provides common operations for dealing with biological sequence data, including data representation and sequence alignment.
TuftsBCB/SMURFBuild
A fork of HMMER-3.0 for the purposes of MRFy and SMURF
TuftsBCB/dsd-functional
Experiments testing ability of DSD to capture functional relationships
TuftsBCB/foods
Our favorite foods.
TuftsBCB/pathway-centrality
A python program that calculates pathway centrality scores for pathway gene sets based on a given ppi networks
TuftsBCB/apps
Library wrappers in Go for computational biology tools that are typically operated from the command line.
TuftsBCB/CANDL_site
TuftsBCB/experiments
A collection of experiments used for both exploratory research and in publications.
TuftsBCB/flib
A command line tool to interface with fragment libraries.
TuftsBCB/FunctionalPath
Building functional path from Gene Ontology hierarchy and evaluate protein function prediction using the paths
TuftsBCB/hhfrag
An implementation of Kalev and Habeck's HHfrag algorithm in Go.
TuftsBCB/Medford-and-Editor-Support-User-Guide
TuftsBCB/pybcb
A small Python module that provides convenience functions for running experiments.
TuftsBCB/structure
A Go library that provides types and functions for common operations on protein structures.
TuftsBCB/tools
A set of command line programs that interface with the repositories in the TuftsBCB organization.