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adage

This is the repository for ADAGE (Analysis using Denoising Autoencoders for Gene Expression)

bis180l_web

Course Website for UC Davis BIS180L

blacklist

Application for making ENCODE Blacklists

chip_annotation

code to annotate a ChIP peak file in BED format (6 columns)

cis-545-big-data-analytics-spring-2018-

CIS 545: Big Data Analytics (Spring 2018)

coge

CoGe (Comparative Genomics) Platform

computational-reagents

Rigor, Reproducibility, Transparency, and Reagent Validity for Computational Biologists

cpython

The Python programming language

danpos3

Updated DANPOS2 to work with python3

deeptools

Tools to process and analyze deep sequencing data.

galaxy

modENCODE Galaxy on Amazon Cloud

gcb_studyguide

Resource for GCB study materials

greenscreenproject

idr

IDR

idr_comparison_pipeline

This code follows ENCODEs pipeline for running IDR (Li et al 2011)

make_our_own_kaggle

Repository for Penn PDSG to Build our Own Kaggle Competition

peakpass

Create ChIP-Seq blacklists automaticaly and validate them.

penndatasci_googlestore_kaggle

Repo for all the Penn Data Science Group to store their scripts and inputs for the Google Store data science competition

phantompeakqualtools

This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.

python_bootcamp

Course materials for 4 week python programming bootcamp at Penn

remap-pipeline

As the ReMap project expands dramatically and regulatory catalogs for other species are requested, it becomes essential to enable joint efforts between the ReMap team and external teams. This is essential for future collaborative production efforts. Briefly, our pipelines uses SnakeMake either in a Conda or Singularity environment depending on the HPC resources, where Torque and Slurm managers are both supported

scipy-cookbook

Scipy Cookbook

spp

SPP - R package for analysis of ChIP-seq and other functional sequencing data

tdmresults

Scripts and data for re-creating TDM results.