For those wishing to install our NG-CHM software locally on their systems or in their bioinformatics pipelines, access to our tools and software can be found in multiple formats and locations.
| Repository | Description |
|---|---|
| NG-CHM | The NG-CHM Heat Map Viewer Source Code. |
| NG-CHM_GUI_BUILDER | Intuitive graphical user interface (GUI) that enables non-experts to create NG-CHMs in a web browser. |
| NG-CHM_Galaxy | Code for a Galaxy tool that creates NGCHM clustered heat maps and a galaxy plugin for dynamically viewing NGCHMs in galaxy. See also: Galaxy Toolshed section below. |
| GenePattern_NGCHM_BasicBuilder | A GenePattern module to build Next-Generation Clustered Heat Map in GenePattern notebook. |
| GenePattern_NGCHM_Viewer | A GenePattern Module to view NGCHM in GenePattern Notebook. |
| NGCHM-R | An R package for creating Next-Generation Clustered Heat Maps (NG-CHM). See also: NGCHMR (CRAN) package link in R Packages section above. |
| NGCHMSupportFiles | Source for R Package containing support files used by NGCHM R package functions chmExportToFile(), chmExportToHTML(), and chmExportToPDF(). See also: NGCHMSupportFiles (R Universe) package link in R Packages section above. |
| NGCHMDemoData | R package containing demonstration data for the NGCHM-R package. See also: NGCHMDemoData (R Universe) package link in R Packages section above. |
| tsvio | R package of utilities for rapidly loading specified rows and/or columns of data from large tab-separated value (tsv) files. See also: tsvio (CRAN) package link in R Packages section above. |
| NG-CHM-Artifacts | This repository contains build artifacts from the NG-CHM Viewer project. |
| acluster | R package for approximate hierarchical clustering. Useful for clustering very large matrices where normal R routines might require too much memory or time to cluster. |
| rstudio-ngchm | rstudio-ngchm is a derivative of rocker/rstudio that includes preinstalled copies of the Next-Generation Clustered Heat Map (NGCHM) viewer and R library. See also: rstudio-ngchm docker container in Docker Containers section below. |
| Tools | Description |
|---|---|
| heat_map_creation | Basic Tool for creating Next-Generation Clustered Heat Maps (NG-CHM). |
| heat_map_creation_advanced | Advanced Tool for creating Next-Generation Clustered Heat Maps (NG-CHM). |
| matrix_manipulation | Matrix manipulation tools |
We’ve created multiple docker containers with preinstalled builders and additional tools for multiple use cases.
| Container | Description |
|---|---|
| ngchm/ngchm | NG-CHM Build Artifacts |
| ngchm/builder | NG-CHM Interactive GUI Builder |
| ngchm/rstudio-ngchm | RStudio container with NG-CHM package preinstalled |
| ngchm/galaxy | An instance of galaxy with the NG-CHM clustered heat map tools included. |
| ngchm/rstudio-ngchm-bioc | R Studio container with Next-Generation Clustered Heat Map package, Bioconductor, and TCGAbiolinks. |
| ngchm/rstudio-ngchm-sc | Variant of ngchm/rstudio-ngchm-bioc with single-cell packages Seurat and singleCellTK installed. |
| ngchm/ngchm-builder-genepattern | A docker images used to build NG-CHMs within the GenePattern environment. |