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anovasplice

aspirin_analysis

Aspirin Data Analysis on RoR

barrel

beers2

beers_simulator

beers_utils

Utilities for the BEERS 2 suite of tools.

bio-cookbooks

A Chef cookbooks repository for bioinformatics tools

biopy-isatab

Python parser for ISAtab, a biological file format for experimental metadata

bp1

bp2

camparee

Configurable And Modular Program Allowing RNA Expression Emulation

chef-cookbooks

Chef cookbooks for various services not directly related to bioinformatics, but are related to it

chronobiome

Adding additional datasets to Amy's chronobiome analyses

collos

CollOS : Collection Of Samples - a lightweight biobanking tool

daemon-kit

Daemon Kit aims to simplify creating Ruby daemons by providing a sound application skeleton (through a generator), task specific generators (jabber bot, etc) and robust environment management code.

decaf

drinc

Duplication Rate Identifier for NGS Cleanup

hogenesch-lab-website

Hogenesch Lab Website

isareport

ISA-Report: Makes nice looking HTML reports from ISA-TAB annotated experiments

isatab-templates

ISATAB XML templates for use in ISACreator

itmat_archive

Simple Rails application to archive the metadata of old experiments (which are on a bunch of disks)

itmat_office_hours

nitecap

Nitecap is an exploratory circadian data analysis tool aimed at high-throughput omics data. It provides a web-interface to examine your dataset with highly-responsive visualizations, allowing the easy viewing of hundreds or thousands of genes or other features. Nitecap computes some standard rhythmicity tests for you, including JTK, ARSER, Lomb-Scargle, Cosinor, and several tests to compare differential rhythmicity across two conditions (such as phase differences).

normalization

RNA-Seq normalization and quantification pipeline

omicsbenchmarkreport

Report template for omics methods benchmarking

pade

Patterns from Gene Expression

pennpipeline

UPENN Proteomics Analysis Pipeline

pgfi-hts

PGFI High Throughput Sequence Center Repo

pre-pade

Pre-PADE

qinteract2

An Application that submits sequest and mascot searches, tpp analyses to a torque queue. Also manages the viewers for analyses results (second iteration)