BiocRevSumm

The intent of this package is to analyze metadata about the series of repositories in review at Bioconductor. We include code to interrogate the contribution issues, summarize package capabilities, and categorize all packages in review. Currently OpenAI LLMs are used to create summaries and classifications of packages.

The listing below is a demonstration created with the package on Nov 19 2025. There are clear deficiencies of labeling, and improved prompting and tooling are needed. Some repositories are excluded because insufficient metadata is present in the DESCRIPTION or README.md.

Example grouping of GitHub Repositories under review at Bioconductor

1. Single-Cell RNA-Seq Analysis

• posDemux: Demultiplexing and filtering sequence reads with combinatorial barcodes.
  • URL: https://github.com/yaccos/posDemux
• fourSynergy: Ensemble algorithm for analyzing 4C-seq data.
  • URL: https://github.com/sophiewind/fourSynergy
• CellMentor: Dimensional reduction using supervised cell type-aware non-negative matrix factorization.
  • URL: https://github.com/petrenkokate/CellMentor/
• hammers: Tools for single-cell RNA sequencing (scRNA-seq) data analysis.
  • URL: https://github.com/andrei-stoica26/hammers

2. Tumor and Mutational Data Simulation

• ClonalSim: Simulating the clonal evolution of tumors with realistic sequencing noise.
  • URL: https://github.com/gbucci/ClonalSim
• MutSeqRData: Experimental data package for mutational sequencing analysis.
  • URL: https://github.com/EHSRB-BSRSE-Bioinformatics/MutSeqRData

3. Metabolomics

• MetaboAnnotatoR: Metabolite annotation of features from Liquid Chromatography-Mass Spectrometry datasets.
  • URL: https://github.com/gggraca/MetaboAnnotatoR
• MetaProViz: Mechanistic hypotheses in metabolomics data by integrating literature.
  • URL: https://github.com/saezlab/MetaProViz
• MetabolomicsPipeline: Analyzing metabolomics data with subpathway analysis and other tools.
  • URL: https://github.com/datalifecycle-ua/MetabolomicsPipeline/

4. Gene and Protein Expression Analysis

• scrapple: Wrappers for single-cell RNA-Seq analysis.
  • URL: https://github.com/libscran/scrapple
• TraianProt: Downstream analysis of quantitative proteomic data.
  • URL: https://github.com/SamueldelaCamaraFuentes/TraianProt
• OAtools: Streamlined analysis of gene expression data on OpenArray platform.
  • URL: https://github.com/uwvirology-ngs/OAtools

5. Chromatin and DNA Interaction

• annoLinker: Annotation of genomic peaks using DNA interaction data.
  • URL: https://github.com/jianhong/annoLinker
• SMTrackR: Visualization of protein-DNA binding states on sequenced DNA molecules.
  • URL: https://github.com/satyanarayan-rao/SMTrackR

6. Genomic Visualization and Enrichment Analysis

• GOfan: Visualization of Gene Ontology enrichment results using sunburst layout.
  • URL: https://github.com/jianhong/GOfan
• ClusterGVis: Clustering and visualization of gene expression data.
  • URL: https://github.com/junjunlab/ClusterGVis
• ImageArray: Handling large image arrays in digital pathology and microscopy.
  • URL: https://github.com/BIMSBbioinfo/ImageArray

7. Data Processing and Pipeline Tools

• tidyprint: Enhancing usability of ‘SummarizedExperiment’ objects within a tidy workflow.
  • URL: https://github.com/tidyomics/tidyprint
• proBatch: Analysis and correction of batch effects in high-throughput experiments.
  • URL: https://github.com/Freddsle/proBatch
• StatescopeR: Discovering cell states from gene expression profiles and bulk RNA.
  • URL: https://github.com/tgac-vumc/StatescopeR

8. Genetic Variation and Splicing Impact

• fRagmentomics: Extraction of fragmentomic features and mutational status from cfDNA.
  • URL: https://github.com/ElsaB-Lab/fRagmentomics
• GXwasR: Conducting sex-aware genetic association analyses in complex traits.
  • URL: https://github.com/boseb/GXwasR
• SpliceImpactR: The impact of alternative RNA splicing on protein structure.
  • URL: https://github.com/fiszbein-lab/SpliceImpactR

9. Machine Learning and Prediction Models

• asuri: Discovery of marker genes for survival and risk prediction.
  • URL: https://github.com/jdelasrivas-lab/asuri
• dioscRi: Deep learning-based tool for clinical prediction in cytometry data.
  • URL: https://github.com/ecool50/dioscRi
• CENTRE: Prediction of cell-type specific enhancer target interactions.
  • URL: https://github.com/slrvv/CENTRE

10. Epigenomics and Transcriptomics Analysis

• epiSeeker: Annotation and visualization of multi-omics epigenetic data.
  • URL: https://github.com/YuLab-SMU/epiSeeker
• decemedip: Deconvoluting cell types in MeDIP-seq data using a Bayesian model.
  • URL: https://github.com/nshen7/decemedip
• HumanRetinaLRSData: Dataset package for RNA sequencing and gene expression analysis.
  • URL: https://github.com/sparthib/HumanRetinaLRSData

11. Variant Representation and Interoperability

• AnVILVRS: Interface to the AnVIL VRS Toolkit for genomic variation representation.
  • URL: https://github.com/Bioconductor/AnVILVRS
• immReferent: Interface for immune receptor (TCR/BCR) and HLA gene IMGT reference data.
  • URL: https://github.com/BorchLab/immReferent

12. Cytometry and Protein Interaction

• CompensAID: Detection of spillover errors in flow cytometry data.
  • URL: https://github.com/Olsman/CompensAID
• SMTrackR: Protein-DNA binding and chromatin accessibility with DamID-seq data.
  • URL: https://github.com/marshall-lab/damidBind