Spatial transcriptomics Optimizing signal and correcting for between-cell-type biases in heterogenous spatial and single-cell RNA-seq SPAMMER: Spatial Analysis of Multi-omics Measurements in R DESpace: a novel analysis framework to discover spatially variable genes Statistical methods for spatial Multiplexed Ion-Beam Imaging data analysis
Spatial transcriptomics Statistical method to rank spatially variable genes adjusted for mean-variance relationship Benchmarking Spot Deconvolution Methods in the Human Dorsolateral Prefrontal Cortex Non-negative spatial matrix factorization for multi-sample spatial transcriptomics data Spatial Multi-omic Profiling of Alzheimer’s Disease in the Human Inferior Temporal Cortex
Single-cell SCArray.sat – Large-scale single-cell RNA-seq data analysis using GDS files and Seurat Comparative analysis of annotation tools in grouping cell types from single cell RNA sequencing data Injecting rigor and reproducibility into CITE-seq workflows: decontamination and in silico gating approaches singlet: Fast, scalable, interpretable, in-core analysis of big single-cell data
Single-cell Unraveling Immunogenomic Diversity in Single-Cell Data Model-based Dimensionality Reduction for Single-cell RNA-seq with Generalized Bilinear Models Interactive analysis of single-cell data using flexible workflows with SCTK2.0 cytofQC: A better way to clean cytof data
RNA-seq Tree-based differential testing using inferential replicate counts for RNASeq Noninvasive, low-cost RNA-sequencing enhances discovery potential of transcriptome studies Preprocessing and analysis of microRNA-seq data lute, a new framework for bulk transcriptomics deconvolution experiments The crisprVerse: a comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies
RNA-seq Genotype calling from Recount3 RNA-seq data catchSalmon/catchKallisto: Dividing out quantification uncertainty allows efficient assessment of differential transcript expression Visualizing genomic characteristics across an RNA-Seq based reference landscape of normal and neoplastic brain Modeling the effects of nicotine and smoking exposures on the developing brain
Outreachy Birds of a Feather Outreachy overview Simplify your BSgenome workflow: Creating BSgenome Data Packages With BSgenomeForge Bringing Sweave Vignettes Into The Modern Age With R Mentoring Opportunities with Outreachy
Microbiome, Proteomics Linear models and empirical Bayes methods for proteome-wide label-free quantification and differential expression in mass spectrometry-based proteomics experiments A novel statistical method for single isoform proteogenomics inference bugphyzz: a harmonized data resource and software for enrichment analysis of microbial physiologies Orchestrating microbiome multi-omics with R/Bioconductor
Infrastructure rworkflows: taming the Wild West of R packages Enabling Reusable and Reproducible Genomic Data Management and Analysis in R BiocPy: enabling Bioconductor workflows in Python CuratedAtlasQueryR: a query API for the CELLxGENE human cell atlas enables defining a body map of immune composition through ageing
Infrastructure GHA-Built: Building binaries for R/Bioconductor packages via Github Actions MultimodalExperiment: Integrative Bulk and Single-Cell Experiment Container AnVILWorkflow: A runnable workflow package for Cloud-implemented analysis pipelines On the Dependency Heaviness of CRAN/Bioconductor Ecosystem
Epigenetics and multi-omics track Standardization of cell-free methylated DNA immunoprecipitation (cfMeDIP) results for population-scale inference Forensics for Multi-Omics Data Generation: Diagnosing and Resolving Mislabeled Samples by Integrating Multiple Data Sources Practical tools for quantitative deidentification and return of results Slicing and dicing aligned genomic and transcriptomic reads for genetic epidemiology
Cancer, Evolution ontoProc - Ontology interfaces for Bioconductor MolEvolvR: A web-app for characterizing proteins using molecular evolution and phylogeny The Mutational Signature Comprehensive Analysis Toolkit (musicatk) for the Discovery, Prediction, and Exploration of Mutational Signatures
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