MD Anderson Cancer Center - Dept. of Bioinformatics and Computational Biology
Tools and projects of BCB at MD Anderson Cancer Center
The University of Texas MD Anderson Cancer Center
Pinned Repositories
BatchEffectsPackage
The MBatch R package and Docker image are designed to help assess and correct for batch effects.
GeneSurvey
Gene Survey R package - take TCGA Standardized Data and make gene level cross-disease and sometimes cross platform comparisons and evaluations simpler to perform
MBatch
Superseded by https://github.com/MD-Anderson-Bioinformatics/BatchEffectsPackage
MetaBatchOmicBrowser
Web application for viewing metabolomics batch effects analyses, as seen at https://bioinformatics.mdanderson.org/MOB/
NG-CHM
A dynamic, graphical environment for exploration of clustered or non-clustered heat map data in a web browser.
NGCHM-R
An R library for creating Next-Generation Clustered Heat Maps (NG-CHM)
ReadMatrixRcpp
R package wrapped around C++ used to quickly read very large "platform" level matrices from within a ZIP archive
SAMMI
SCLC-Cancer-Cell-Manuscript
SpliceSeq
A tool for investigating alternative mRNA splicing in next generation mRNA sequence data.
MD Anderson Cancer Center - Dept. of Bioinformatics and Computational Biology's Repositories
MD-Anderson-Bioinformatics/BatchEffectsPackage
The MBatch R package and Docker image are designed to help assess and correct for batch effects.
MD-Anderson-Bioinformatics/NG-CHM
A dynamic, graphical environment for exploration of clustered or non-clustered heat map data in a web browser.
MD-Anderson-Bioinformatics/NGCHM-R
An R library for creating Next-Generation Clustered Heat Maps (NG-CHM)
MD-Anderson-Bioinformatics/MetaBatchOmicBrowser
Web application for viewing metabolomics batch effects analyses, as seen at https://bioinformatics.mdanderson.org/MOB/
MD-Anderson-Bioinformatics/SCLC-Cancer-Cell-Manuscript
MD-Anderson-Bioinformatics/EGFR-Structure-Function-Nature-Manuscript
MD-Anderson-Bioinformatics/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.
MD-Anderson-Bioinformatics/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".
MD-Anderson-Bioinformatics/BatchEffectsInterfaceStack
Docker Compose Stack for running Batch Effects Interface
MD-Anderson-Bioinformatics/BatchEffectsPackageData
Data Repo for BatchEffectsPackage
MD-Anderson-Bioinformatics/BCBBuildDocs
Documentation for GitLab CI/CD with Docker
MD-Anderson-Bioinformatics/DataAPI
DataAPI is a project for accesing and viewing the data and analysis (particulary of Batch Effects) of large datasets in Standardized Data format.
MD-Anderson-Bioinformatics/ldap-jwt
Lightweight node.js based web service that provides user authentication against LDAP server (Active Directory / Windows network) credentials and returns a JSON Web Token.
MD-Anderson-Bioinformatics/MD-Anderson-Bioinformatics.r-universe.dev
MD-Anderson-Bioinformatics/Neoimmuno
MD-Anderson-Bioinformatics/NG-CHM_GUI_BUILDER
Simple graphical builder for Next-Generation Clustered Heat Maps
MD-Anderson-Bioinformatics/SCLC_Subtyping
MD-Anderson-Bioinformatics/StandardizedData
Code and packages for Standardized Data format for large scale studies.
MD-Anderson-Bioinformatics/tsvio
R library for reading (subsets of) tsv files
MD-Anderson-Bioinformatics/GenePattern_NGCHM_Viewer
A GenePattern Module to view NGCHM in GenePattern Notebook
MD-Anderson-Bioinformatics/NG-CHM-Viewer-Source-Documentation
MD-Anderson-Bioinformatics/acluster
R package for approximate hierarchical clustering.
MD-Anderson-Bioinformatics/MBatchImage
Superseded by https://github.com/MD-Anderson-Bioinformatics/BatchEffectsPackage
MD-Anderson-Bioinformatics/NG-CHM-Artifacts
MD-Anderson-Bioinformatics/NG-CHM_Galaxy
Next-Generation Clustered Heat Maps for Galaxy
MD-Anderson-Bioinformatics/NGCHMDemoData
Demo Data for NGCHM R package.
MD-Anderson-Bioinformatics/NGCHMSupportFiles
Support files for NGCHM-R package
MD-Anderson-Bioinformatics/pathway-mapper
An interactive and collaborative graphical curation tool for cancer pathways
MD-Anderson-Bioinformatics/ScatterPlotPlugin
NG-CHM plugin for making 2-D scatter plots
MD-Anderson-Bioinformatics/ScatterPlotPlugin3D
An NG-CHM panel plugin for three-dimensional scatter plots.