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cytoviewer: an R/Bioconductor package for interactive visualization and exploration of highly multiplexed imaging data
BackgroundHighly multiplexed imaging enables single-cell-resolved detection of numerous biological molecules in their spatial tissue context....
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spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data
BackgroundSpatially-resolved transcriptomics has now enabled the quantification of high-throughput and transcriptome-wide gene expression in intact...
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DNAfusion: an R/Bioconductor package for increased sensitivity of detecting gene fusions in liquid biopsies
BackgroundEML4-ALK gene fusions are oncogenic drivers in non-small cell lung cancer (NSCLC), and liquid biopsies containing EML4-ALK fragments can...
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CytoPipeline and CytoPipelineGUI: a Bioconductor R package suite for building and visualizing automated pre-processing pipelines for flow cytometry data
BackgroundWith the increase of the dimensionality in flow cytometry data over the past years, there is a growing need to replace or complement...
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rprimer: an R/bioconductor package for design of degenerate oligos for sequence variable viruses
BackgroundThis paper presents a new R/Bioconductor package, rprimer, for design of degenerate oligos and PCR assays for sequence variable viruses. A...
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mirTarRnaSeq: An R/Bioconductor Statistical Package for miRNA-mRNA Target Identification and Interaction Analysis
We introduce mirTarRnaSeq , an R/Bioconductor package for quantitative assessment of miRNA-mRNA relationships within sample cohorts. mirTarRnaSeq is a...
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FindIT2: an R/Bioconductor package to identify influential transcription factor and targets based on multi-omics data
BackgroundTranscription factors (TFs) play central roles in regulating gene expression. With the rapid growth in the use of high-throughput...
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GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data
BackgroundThe interpretation of results from transcriptome profiling experiments via RNA sequencing (RNA-seq) can be a complex task, where the...
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BiocMAP: a Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data
BackgroundBisulfite sequencing is a powerful tool for profiling genomic methylation, an epigenetic modification critical in the understanding of...
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BioNERO: an all-in-one R/Bioconductor package for comprehensive and easy biological network reconstruction
Currently, standard network analysis workflows rely on many different packages, often requiring users to have a solid statistics and programming...
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ideal: an R/Bioconductor package for interactive differential expression analysis
BackgroundRNA sequencing (RNA-seq) is an ever increasingly popular tool for transcriptome profiling. A key point to make the best use of the...
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RGMQL: scalable and interoperable computing of heterogeneous omics big data and metadata in R/Bioconductor
BackgroundHeterogeneous omics data, increasingly collected through high-throughput technologies, can contain hidden answers to very important and...
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GWENA: gene co-expression networks analysis and extended modules characterization in a single Bioconductor package
BackgroundNetwork-based analysis of gene expression through co-expression networks can be used to investigate modular relationships occurring between...
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ReUseData: an R/Bioconductor tool for reusable and reproducible genomic data management
BackgroundThe increasing volume and complexity of genomic data pose significant challenges for effective data management and reuse. Public genomic...
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Chemical map-based prediction of nucleosome positioning using the Bioconductor package nuCpos
BackgroundAssessing the nucleosome-forming potential of specific DNA sequences is important for understanding complex chromatin organization. Methods...
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CytoTree: an R/Bioconductor package for analysis and visualization of flow and mass cytometry data
BackgroundThe rapidly increasing dimensionality and throughput of flow and mass cytometry data necessitate new bioinformatics tools for analysis and...
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GenomicDistributions: fast analysis of genomic intervals with Bioconductor
BackgroundEpigenome analysis relies on defined sets of genomic regions output by widely used assays such as ChIP-seq and ATAC-seq. Statistical...
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geneExpressionFromGEO: An R Package to Facilitate Data Reading from Gene Expression Omnibus (GEO)
Gene expression profiling is a useful way to measure the activity of genes in molecular biology and, because of its effectiveness, researchers have...
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CeTF: an R/Bioconductor package for transcription factor co-expression networks using regulatory impact factors (RIF) and partial correlation and information (PCIT) analysis
BackgroundFinding meaningful gene-gene interaction and the main Transcription Factors (TFs) in co-expression networks is one of the most important...
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PRANA: an R package for differential co-expression network analysis with the presence of additional covariates
BackgroundAdvances in sequencing technology and cost reduction have enabled an emergence of various statistical methods used in RNA-sequencing data,...
