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2017-statefarm-codingcompetitionproblem

Welcome to the 2017 State Farm Java Coding Competition. If you have questions during the coding competition, please contact [email protected] or you can submit an issue through GitHub. Please take a look at IT employment opportunities at State Farm by visiting www.statefarm.com/IT.

abc-enhancer-gene-prediction

Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)

alarmapplication

alarmapplication2

applicationtestingmodule

Framework to test any API's for the Hack Day idea

atles-dmelanogaster

A system for automated, high-throughput, realtime observation and conditioning experiments for Drosophila melanogaster (fruit fly)

bash-personal-site

Basheer's Personal Site

bash-roster-repo

biojs

A library of JavaScript components to represent biological data

biojs-rest-flytranscription

BioJS JavaScript package for interaction with the FlyMine (Intermine) service

biotools

Web application that analyzes the reverse complement of a molecular sequence

blastplusplus

Upgrading NCBI's BLAST tool

bluetoothpopquiz

bmif_pset1

cellx-postcomfirmation-pg-layer

AWS Lambda Node.JS layer containing postegresql package for the AWS Cognito Post-Confirmation trigger

chtml-transcriptor

Convert a directory of composite HTML files (.chtml files) to the standard .html files

classqs

classqs-webapp

Class-Qs web application

clubgame

Programming Club Game

cn-core-hpc-processing

Folder in BnB - UGE scripts to retrieve cores/artifacts form human normal and human tumor samples.

cn-ml-analysis

Machine learning analysis of genomic copy number features

cnfe-library

copy number feature extraction library

cnprep

:exclamation: This is a read-only mirror of the CRAN R package repository. CNprep — Pre-process DNA Copy Number (CN) Data for Detection of CN Events

cnprep-core-analysis

Run CORE on CNprep output

cnprep-event-slicing

Taking CNprep output and slicing clusters into aberration events

cnprep-hpc-clustering

Using CNprep to cluster segments generated by FACETS

cnprep-slicing-core-analysis

From the splicing output of the CNprep results, feed the splicing event regions as inputs to CORE to determine recurrent alteration events

cnv-clinical-preprocessing

Subset of scripts created during the CSHL URP 2018. Developing method to extract predictive biomarkers from PDAC patient derived organoids. Using COREs from CNV and WES data from pancreatic tumor organoids to predict chemotherapeutic drug response. This repository investigates copy number preprocessing tools and also preprocesses genomic features for ML analysis.

cnvkit-workflow-adapter

Contains source code to easily include the CNVkit data into the process workflow

cnvkit_cnprep_clustering

CNprep clustering on data from CNVkit copy number profiles