Krishnan Lab

PecanPy

A fast, parallelized, memory efficient, and cache-optimized Python implementation of node2vec

teaching

Courses & workshops led by members of the Krishnan Lab.

txt2onto

Code for classifying unstructured text to tissue ontology terms using natural language processing and machine learning.

obnb

A Python toolkit for setting up benchmarking dataset using biomedical networks

PyGenePlexus

A network based gene classification library to generate genome wide predictions about genes that are functionally similar to the input gene list.

GenePlexus

Data, results, and code accompanying the manuscript: "Supervised learning is an accurate method for network-based gene classification"

NetworkLearningEval

See https://github.com/krishnanlab/obnb

RNAseq_coexpression

In-depth analysis of normalization and transformation methods for building coexpression networks from RNA-seq data.

Expresto

Data, results, and code accompanying the manuscript: "A Flexible, Interpretable, and Accurate Approach for Imputing the Expression of Unmeasured Genes" "

PecanPy_benchmarks

cone

COntext-specific Network Embedding

MCC-F1-Curve-and-Metrics

MCC-F1 curve: a performance evaluation technique for binary classification

node2vecplus_benchmarks

obnbench

Benchmarking repository for OBNB

pydab

A _blazingly fast_ Python package for modifying and converting DAB files

talks

Slides and materials from talks, workshops, seminars, etc.

ASD-gene-prediction-Krishnan2016

Weighted Learning on ASD data

chronic-inflammation

Source code for "A network-based approach for isolating the chronic inflammation gene signatures underlying complex diseases towards finding new treatment opportunities"

geneplexus_app

Age-sex_signatures_in_humans_code

code for Human pan-body age- and sex-specific molecular phenomena inferred from public transcriptome data using machine learning

ECRE_student

Student repository for ECRE workshops and research experience

gene-plexus

WIP new gene plexus app

GenePlexusZoo-Mancusript

Repository Accompanying the manuscript J"oint representation of molecular networks from multiple species improves gene classification"

gp-gcp-frontend

This repo will test getting a GitHub page site talk to google cloud

simplex

Simplex app