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GEM software suite (GEM, GPS, KMAC, KSM, RMD, etc.)
Perform hyper-parameter tuning, training, testing and prediction with Keras
Launch scripts and containers for our Jupyterhub server.
Opinionated stacks of ready-to-run Jupyter applications in Docker. Forked to add GPU capabilities.
The source code for GERV method
DEPRECATED. Multi-user server for Jupyter notebooks. Forked to add client certificate authentication.
A tool that lauches docker jobs on Amazon EC2.
Winner algorithm for CAGI4 eQTL-causal SNP challenge
kmer model launch scripts
Docker image for running DeepSEA for predicting
Docker image for the DeepSEA method.
Wrapper integrating Mri and caffe-cnn
Caffe-based convolutional neural network
Simple method to protect web content by group name on CSAIL servers.
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis. Forked to get automated Docker builds.
Docker image for the DeepBind method.
Automated discovery of functional generality of gene expression
High resolution peak calling and motif discovery for ChIP-seq and ChIP-exo data
High Resolution Modeling of Chromatin Interactions
A Docker container that properly handles signals and will run in SGE.
Track and respond to email list messages.
Misc tools for dealing with shortreads and bams