tuftsbcb Goto Github PK

apps

Library wrappers in Go for computational biology tools that are typically operated from the command line.

candl_site

dazzle

detangle-cd

Code for Hall-Swan et al. 2017, "Detangling PPI networks to uncover functionally meaningful clusters"

dsd-functional

Experiments testing ability of DSD to capture functional relationships

experiments

A collection of experiments used for both exploratory research and in publications.

flib

A command line tool to interface with fragment libraries.

foods

Our favorite foods.

fragbag

A fast implementation of FragBag for protein structures and sequences.

functionalpath

Building functional path from Gene Ontology hierarchy and evaluate protein function prediction using the paths

git-tutorial

A git-by-example tutorial that demonstrates basic git commands and pushing to GitHub repositories.

hhfrag

An implementation of Kalev and Habeck's HHfrag algorithm in Go.

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-and-editor-support-user-guide

medford-examples

Example MEDFORD metadata files for a variety of datatypes

medford-language-server

A language server, implementing the Language Server Protocol, for the MEDFORD metadata markup language.

medford-spec

medford-vscode

The VS Code extension that supports the MEDFORD metadata markup language

pathway-centrality

A python program that calculates pathway centrality scores for pathway gene sets based on a given ppi networks

pybcb

A small Python module that provides convenience functions for running experiments.

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.

smurfbuild

A fork of HMMER-3.0 for the purposes of MRFy and SMURF

structure

A Go library that provides types and functions for common operations on protein structures.

tools

A set of command line programs that interface with the repositories in the TuftsBCB organization.

walker

Python implementation of Kohler et al.'s random walk with restart