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**Upcoming Conferences**: - EuroBioC2025 (Sep 17-19, Barcelona). The Bioconductor project develops and supports free open-source software for the rigorous and reproducible analysis of biological data, focusing on R and statistical methods. We foster a diverse, collaborative, and welcoming community of developers and data scientists. Founded in 2001, Bioconductor is an open-source software project widely used in bioinformatics and biomedical research. It hosts over 2,000 R packages contributed by over 1,000 developers, with over 40 million downloads per year. Bioconductor has been cited in more than 60,000 scientific publications. Bioconductor operates with two releases each year and has an active user community. It is also available as Docker images. The project is overseen by a Core team based primarily in Boston, with members from US and international institutions. Our Community and Technical Advisory Boards, along with various Committees and Working Groups, are largely composed of dedicated volunteers who support our mission and ensure long-term viability. #Bioinformatics #OpenSource #BioconductorCommunity #RStats #GBCC2025 #EuroBioC2025
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Application note: TDbasedUFE and TDbasedUFEadv: bioconductor packages to perform tensor decomposition based unsupervised feature extraction - Frontiers

Application note: TDbasedUFE and TDbasedUFEadv: bioconductor packages to perform tensor decomposition based unsupervised feature extraction Frontiers

spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data - BMC Genomics

spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data BMC Genomics

Orchestrating chromosome conformation capture analysis with Bioconductor - Nature

Orchestrating chromosome conformation capture analysis with Bioconductor Nature

Analysis workflow of publicly available RNA-sequencing datasets - ScienceDirect.com

Analysis workflow of publicly available RNA-sequencing datasets ScienceDirect.com

GenomicDistributions: fast analysis of genomic intervals with Bioconductor - BMC Genomics

GenomicDistributions: fast analysis of genomic intervals with Bioconductor BMC Genomics

Rvisdiff: An R package for interactive visualization of differential expression - Frontiers

Rvisdiff: An R package for interactive visualization of differential expression Frontiers

A comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies - Nature

A comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies Nature

Network analysis of TCGA and GTEx gene expression datasets for identification of trait-associated biomarkers in human cancer - ScienceDirect.com

Network analysis of TCGA and GTEx gene expression datasets for identification of trait-associated biomarkers in human cancer ScienceDirect.com

ideal: an R/Bioconductor package for interactive differential expression analysis - BMC Bioinformatics

ideal: an R/Bioconductor package for interactive differential expression analysis BMC Bioinformatics

cytoviewer: an R/Bioconductor package for interactive visualization and exploration of highly multiplexed imaging data - BMC Bioinformatics

cytoviewer: an R/Bioconductor package for interactive visualization and exploration of highly multiplexed imaging data BMC Bioinformatics

CAGEfightR: analysis of 5′-end data using R/Bioconductor - BMC Bioinformatics

CAGEfightR: analysis of 5′-end data using R/Bioconductor BMC Bioinformatics

GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data - BMC Bioinformatics

GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data BMC Bioinformatics

FindIT2: an R/Bioconductor package to identify influential transcription factor and targets based on multi-omics data - BMC Genomics

FindIT2: an R/Bioconductor package to identify influential transcription factor and targets based on multi-omics data BMC Genomics

ReUseData: an R/Bioconductor tool for reusable and reproducible genomic data management - BMC Bioinformatics

ReUseData: an R/Bioconductor tool for reusable and reproducible genomic data management BMC Bioinformatics

GWENA: gene co-expression networks analysis and extended modules characterization in a single Bioconductor package - BMC Bioinformatics

GWENA: gene co-expression networks analysis and extended modules characterization in a single Bioconductor package BMC Bioinformatics

scruff : an R/Bioconductor package for preprocessing single-cell RNA-sequencing data - BMC Bioinformatics

scruff : an R/Bioconductor package for preprocessing single-cell RNA-sequencing data BMC Bioinformatics

RGMQL: scalable and interoperable computing of heterogeneous omics big data and metadata in R/Bioconductor - BMC Bioinformatics

RGMQL: scalable and interoperable computing of heterogeneous omics big data and metadata in R/Bioconductor BMC Bioinformatics

fcScan: a versatile tool to cluster combinations of sites using genomic coordinates - BMC Bioinformatics

fcScan: a versatile tool to cluster combinations of sites using genomic coordinates BMC Bioinformatics

miRBaseConverter: an R/Bioconductor package for converting and retrieving miRNA name, accession, sequence and family information in different versions of miRBase - BMC Bioinformatics

miRBaseConverter: an R/Bioconductor package for converting and retrieving miRNA name, accession, sequence and family information in different versions of miRBase BMC Bioinformatics

SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering - BMC Bioinformatics

SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering BMC Bioinformatics

COCOA: coordinate covariation analysis of epigenetic heterogeneity - Genome Biology

COCOA: coordinate covariation analysis of epigenetic heterogeneity Genome Biology

CeTF: an R/Bioconductor package for transcription factor co-expression networks using regulatory impact factors (RIF) and partial correlation and information (PCIT) analysis - BMC Genomics

CeTF: an R/Bioconductor package for transcription factor co-expression networks using regulatory impact factors (RIF) and partial correlation and information (PCIT) analysis BMC Genomics

CytoTree: an R/Bioconductor package for analysis and visualization of flow and mass cytometry data - BMC Bioinformatics

CytoTree: an R/Bioconductor package for analysis and visualization of flow and mass cytometry data BMC Bioinformatics

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics - BMC Genomics

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics BMC Genomics

diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering | Communications Biology - Nature

diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering | Communications Biology Nature

multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data - BMC Bioinformatics

multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data BMC Bioinformatics

A comparison of strategies for generating artificial replicates in RNA-seq experiments - Nature

A comparison of strategies for generating artificial replicates in RNA-seq experiments Nature

RnaSeqSampleSize: real data based sample size estimation for RNA sequencing - BMC Bioinformatics

RnaSeqSampleSize: real data based sample size estimation for RNA sequencing BMC Bioinformatics

plyranges: a grammar of genomic data transformation - Genome Biology

plyranges: a grammar of genomic data transformation Genome Biology

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