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bioagents

Biological reasoning agents

bioservices

Access to Biological Web Services from Python.

books

code

Compilation of R and Python programming codes on the Data Professor YouTube channel.

coewc

Script for paper of a new method for the discovery of essential proteins-PLoS One 2013

dcell

DCell browser and gene deletion simulator

deepconv-dti

deepdta

deepep

deepgo

Function prediction using a deep ontology-aware classifier

deephe

A deep learning framework for essential gene prediction

deeplearning-biology

A list of deep learning implementations in biology

deepsf

A deep learning framework for essential gene prediction

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

gogan

hic-pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing

hicplus

ipython

Official repository for IPython itself. Other repos in the IPython organization contain things like the website, documentation builds, etc.

mdnnmd

An implementation of multimodal deep neural network, a new model for human breast cancer prognosis prediction.

moproembeddings

Implementation of moment propagation embeddings.

network_evaluation_tools

Python 2.7 package with examples for evaluating a network's ability to group a given node set in network proximity.

node2vec

Implementation of the node2vec algorithm.

ogn

Script for paper Predicting essential proteins by integrating orthology, gene expressions, and PPI networks http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0195410.

predcan

Ontology-based prediction of cancer driver genes

pygat

Pytorch implementation of the Graph Attention Network model by Veličković et. al (2017, https://arxiv.org/abs/1710.10903)

pypathway

A python package for pathway visualization

single-cell-tutorial

Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"

tfagent

Search for targets for given transcription factor and vice versa, and much more.

yolov3

YOLOv3 in PyTorch > ONNX > CoreML > iOS