MD Anderson Cancer Center - Dept. of Bioinformatics and Computational Biology's repositories
BatchEffectsPackage
The MBatch R package and Docker image are designed to help assess and correct for batch effects.
MetaBatchOmicBrowser
Web application for viewing metabolomics batch effects analyses, as seen at https://bioinformatics.mdanderson.org/MOB/
MetaBatchAnalyzer
Turnkey Docker Stack system for evaluating and visualizing batch effects in metabolomics data, with the ability to download data from Metabolomics Workbench for analysis.
rppaspace
Reverse-Phase Protein Array Super Position and Concentration EvaluationThe RPPASPACE R package provides tools for the analysis of reverse-phase protein arrays (RPPAs), which are also known as "tissue lysate arrays" or simply "lysate arrays". The package's primary purpose is to input a set of quantification files representing dilution series of samples and control points taken from scanned RPPA slides and determine a relative log concentration value for each valid dilution series present in each slide and provide graphical visualization of the input and output data and their relationships. Other optional features include generation of quality control scores for judging the quality of the input data, spatial adjustment of sample points based on controls added to the slides, and various types of normalization of calculated values across a set of slides. The package was derived from a previous package called SuperCurve. For a detailed description of data inputs and outputs and usage information see the vignette "Guide_to_RPPASPACE".
BatchEffectsInterfaceStack
Docker Compose Stack for running Batch Effects Interface
BatchEffectsPackageData
Data Repo for BatchEffectsPackage
BCBBuildDocs
Documentation for GitLab CI/CD with Docker
NG-CHM_GUI_BUILDER
Simple graphical builder for Next-Generation Clustered Heat Maps
StandardizedData
Code and packages for Standardized Data format for large scale studies.
GenePattern_NGCHM_Viewer
A GenePattern Module to view NGCHM in GenePattern Notebook
MBatchImage
Superseded by https://github.com/MD-Anderson-Bioinformatics/BatchEffectsPackage
NG-CHM_Galaxy
Next-Generation Clustered Heat Maps for Galaxy
NGCHMDemoData
Demo Data for NGCHM R package.
NGCHMSupportFiles
Support files for NGCHM-R package
pathway-mapper
An interactive and collaborative graphical curation tool for cancer pathways
ScatterPlotPlugin
NG-CHM plugin for making 2-D scatter plots
ScatterPlotPlugin3D
An NG-CHM panel plugin for three-dimensional scatter plots.