knoweng.github.io

Here are the KnowEnG repos. For more information about the KnowEnG platform, or to sign up for an account, visit the KnowEnG site.

Platform Interface

• platform: Web services and client for the KnowEnG platform
• quickstart-demos: Sample files and readmes for analytics pipelines on KnowEnG platform

Analysis Pipeline

• GeneSet_Characterization_Pipeline: Ranks a user supplied gene set against KnowEnG’s gene sets collection
• Gene_Prioritization_Pipeline: Network-based prioritization of genes associated with phenotypes
• Feature_Prioritization_Pipeline: General purpose features prioritization pipeline
• Simplified_InPheRNo_Pipeline: Identifies ‘phenotype-relevant’ transcriptional regulatory networks
• Samples_Clustering_Pipeline: Clusters the sample-based columns of a spreadsheet whose rows correspond to genes
• General_Clustering_Pipeline: Clusters columns of any data frame
• Clustering_Evaluation: Evaluates the clustering result of KnowEnG’s Samples Clustering Pipeline
• Signature_Analysis_Pipeline: Gene signature similarity analysis
• Phenotype_Prediction_Pipeline: Regression to infer an ‘omic’-phenotype association
• Spreadsheets_Transformation: Apply various transformations (transpose, merge, ….) on one or more DataFrames
• Data_Cleanup_Pipeline: Maps gene-label row names of a spreadsheet to Ensembl names and checks data formats
• KnowEnG_Pipelines_Library: Python scripts to support KnowEnG pipelines

Common Workflow Language (CWL) Descriptions

• KnowEnG_CWL: CWL for KnowEnG pipelines for cwltool and CGC

Knowledge Network

• KnowNet_Pipeline_Tools: Setup resources and start KN_Builder
• KN_Builder: Fetch and parse source files to construct KnowEnG Knowledge Network
• KN_Fetcher: Download a subnetwork from the KnowEnG Knowledge Network
• KN_Mapper: Maps names to entity IDs in the KnowEnG Knowledge Network

Education

• TeachEnG: A Teaching Engine for Genomics
• ClusterEnG: Educational web resource for clustering and visualizing high-dimensional data
• SequencEnG: An interactive learning resource for next-generation sequencing (NGS) techniques

Research

• DRaWR: Discriminative Random Walk with Restart
• ProGENI: Prioritization of Genes Enhanced with Network Information
• pgenmi: Probabilistic Gene Expression in the Middle Analysis
• clusDCA: Software to accompany ISMB2015 paper
• PACER: PACER tool for pathway identification from chemosensitivity data
• Simplified-InPheRNo: This is the simplified version of InPheRNo

This site is open source. Improve this page.