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openrefine

OpenRefine is a free, open source power tool for working with messy data and improving it

orbweaver

A convolutional neural network for predicting chromatin accessibility in multiple cell types from DNA sequence

orna

Fast in-silico normalization algorithm for NGS data

outrigger

Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data

pairsamtools

CLI tools to process mapped Hi-C data

pathcore-t

Methods to build a network of pathway co-occurrence relationships out of expression signatures extracted from transcriptomic compendia.

pathos

parallel graph management and execution in heterogeneous computing

pedla

PEDLA: predicting enhancers with deep learning-based algorithmic framework

pfs

A git-like distributed file system for a Dockerized world.

phate

PHATE dimensionality reduction method

phenomenal-h2020

Documentation and wiki for the PhenoMeNal H2020 E-Infrastructure Project

phyx

phylogenetics tools for linux (and other mostly posix compliant) computers

pinchesandcacti

Library for constructing pinch graphs and cactus graphs

pindel

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

pipelines-cwl

Pipelines developed and used by 4DN-DCIC in Common Workflow Language

pix2pixbegan.pytorch

A pytorch implementation of pix2pix + BEGAN (Boundary Equilibrium Generative Adversarial Networks)

ppca

Probabilistic Principal Component Analysis

practical-pytorch

PyTorch tutorials demonstrating modern techniques with readable code

predcircrna

predicting circularRNA from other long non-coding RNA using machine learning

prostate_hic

Analysis of prostate cancer chromatin spatial organization

ptero

ptero-workflow

Client-facing API for the PTero system

pufferfish

An efficient index for the colored, compacted, de Bruijn graph

py2bit

A python library for accessing 2bit files

pybigwig

A python extension for quick access to bigWig and bigBed files

pyboost

modular 2D boosting code with stabilization and hierarchies

pyclustering

pyclustring is a Python, C++ data mining (clustering, oscillatory networks, neural networks, etc.) library.

pydata-book

Materials and IPython notebooks for "Python for Data Analysis" by Wes McKinney, published by O'Reilly Media

pydeep

pydown

An HTML5 presentation builder written by python