Comprehensive Hub for Alternative Regulatory Mapping (CHARM)
CHARM is an R Shiny web application for exploring the regulatory roles of RNA-binding proteins (RBPs) in gene expression, splicing regulation, and direct RNA binding.
The app integrates data from the ENCODE project (Luo et al., 2020), including eCLIP and RNA-seq datasets from RBP knockdown/knockout experiments in HEPG2 (liver cancer) and K562 (leukaemia) cell lines.
CHARM serves as both a repository of this curated data and a discovery tool:
- Explore how 168 RBPs from ENCODE affect expression, splicing, and binding.
- Infer potential networks between these regulatory layers, revealing new pathways and mechanisms.
- Upload your own expression, splicing, or binding datasets to identify RBPs most likely altered in your system.
CHARM integrates three main data types:
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Expression: Differential expression upon RBP knockdown/knockout, with pathway-level insights from Gene Set Enrichment Analysis.
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Splicing: Alternative splicing changes quantified with betAS (Ferreira et al., 2024), using VastDB nomenclature (Tapial et al., 2017).
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Binding: Altered RNA binding patterns of the silenced RBP and other RBPs, characterized with the eCLIPSE tool (see below).
eCLIPSE is a companion tool that processes eCLIP data from ENCODE to generate RNA splicing maps. It aligns binding profiles to the genomic coordinates of splicing events defined in VastDB (Tapial et al., 2017).
This allows assessment of how each RBP regulates splicing events both directly (through its own binding) and indirectly (through effects on other RBPs).
eCLIPSE was used to generate the binding layer in CHARM. The tool is freely available and can also be applied to user-submitted eCLIP datasets to map splicing regulation of additional RBPs.
Full tutorials are published at diseasetranscriptomicslab.github.io/CHARM:
- CHARM App Tutorial : using the Shiny app itself, no code required.
- eCLIPSE Local Pipeline : running eCLIPSE outside the app: building your own splicing genome (VAST-TOOLS/VastDB or rMATS), intersecting it with your own eCLIP peaks, and generating RNA binding maps.
Source for both lives in docs/.
| Path | What it is |
|---|---|
app.R |
The CHARM Shiny app itself (UI + server). |
helper_functions.R |
Shared R functions used by app.R : data loading, statistics, and plotting (RNA binding maps, heatmaps, network views, etc.). |
Dockerfile, .dockerignore |
Container build for deploying the app. |
www/ |
Static assets served by the Shiny app (logo). |
Images/ |
Screenshots and figures used in documentation/READMEs. |
example_data/ |
Small example input files for trying the app's Discovery-mode upload features. |
eCLIPSE/ |
The eCLIPSE pipeline: preprocessing scripts (Eclip_preprocessing_*.R, eCLIPSE_Exon.py, eCLIPSE_Intron.py), the RNA-binding-map notebooks (Eclip_position_matrix.Rmd, eCLIPSE_plotting_functions.Rmd), and small reference tables. Some raw event tables here are too large for git. See Large data files. See eCLIPSE/README.md for details on running the pipeline. |
Markdowns/ |
Supplementary R Markdown notebooks documenting each app module (Expression, Splicing, Binding) and the original eCLIPSE analysis notebook these pipeline scripts were extracted from. |
docs/ |
The GitHub Pages documentation site (app tutorial + eCLIPSE local-pipeline tutorial) and downloadable user-facing docs (.docx). |
LocalJob_File*.R, app_binding_similar_patches.R, *_all_vs_all.py |
One-off/personal analysis and patch scripts used during development; not part of the app or pipeline proper. |
LICENSE, DESCRIPTION, NAMESPACE, CHARM.Rproj |
R package/project metadata. |
A few files are intentionally excluded from git (see .gitignore) because they exceed or approach GitHub's 100 MB per-file limit: the data/ folder (precomputed app data, several files close to 1 GB) and four raw eCLIPSE event tables (eCLIPSE/all_data_combined_38.txt, eCLIPSE/BigExon_events.txt, eCLIPSE/Exon_events_Rmats.txt, eCLIPSE/Intron_events.txt). These are distributed via Zenodo instead. See the Zenodo record for download links, or regenerate them from ENCODE/VastDB following eCLIPSE/README.md.