Centralized Tools
Data Collection and Storage Tools
OpenSpecimen
OpenSpecimen is a biobanking informatics platform that streamlines the process of collecting high quality standards-based (SNOMED, LOINC, ICD, etc.) data, and allows users to collect disease-specific annotations, clinical and pathology data, study-specific parameters, patient questionnaires, QA/QC data, specimen lifecycle events, and any other site-specific custom data.
RedCap
REDCap is a secure web application for building and managing online surveys and databases. It is specifically geared to support online or offline data capture for research studies and operations (including 21 CFR Part 11, FISMA, and HIPAA-compliant environments).
i2b2
I2B2 is a data warehouse platform which can integrate person-oriented clinical data, trials data, genotypic data, and knowledge annotation. Data in multiple I2B2 databases of different projects can be stored to an enterprise shared database.
Online Tools
Clinical Variable-Based Analysis
Group Survival Analysis
Group Survival Analysis perform analysis based on various clinical categorical variables.
Individual Gene-Level Analysis
Gene Based Survival Analysis
Gene Based Survival Analysis perform analysis based on gene expression (High vs Low) or mutation status (Mut vs WT).
Expression Profile Comparison Analysis
Expression Profile Comparison Analysis compares gene expression between two selected groups.
Copy Number Variation vs Expression Analysis
Copy Number Variation vs Expression Analysis compares gene expression among cnv gain, cnv dipole, and cnv loss.
Methylation vs Expression Analysis
Methylation vs Expression Analysis compares gene expression between methylation and no methylation.
Meta Analysis - Tumor vs Normal
Meta Analysis - Tumor vs Normal effectively combines the statistical strength from multiple data sets which allows greater precision than using any of the single studies. We provide forest plots to summarize tumor - normal standardized mean difference.
Meta Analysis - Survival
Meta Analysis - Survival effectively combines the statistical strength from multiple data sets which allows greater precision than using any of the single studies. We provide forest plots to summarize hazard ratios for survival meta-analysis.
Gene Set Analysis
Coexpression Heatmap Analysis
Perform analysis based on clinical categorical variables.
Web Service APIs
Data Transfer
Download Data
Download Data Web Service API provides functions of getting clinical, sample, genomic, and imaging data from our pediatric data commons.
Upload Data
Upload Data Web Service API provides functions of uploading clinical, sample, genomic, and imaging data into our pediatric data commons.
Extract Clinical Text
NLP - Extract Clinical Text
NLP - Extract Clinical Text Web Service API provides functions of extracting valuable clinical text information from electrical text document.
Downloadable Packages
Data Curation
NLP - Extract Clinical Text
NLP - Extract Clinical Text Software Package provides functions of extracting valuable clinical text information from electrical text document.
Data Processing
Pipeline 1
Pipeline 1 processes genomic data.
Pipeline 2
Pipeline 2 processes genomic data.
Data Modeling
Modeling Algorithm 1
Modeling Algorithm 1 establishes a predictive model for survival rate.
Modeling Algorithm 2
Modeling Algorithm 2 identifies tumor types in tissue image.