ArticleBMC bioinformatics2021
Searchlight: automated bulk RNA-seq exploration and visualisation using dynamically generated R scripts.
Article in BMC bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Acute TGFα drives OA-associated transcriptional and metabolic remodelling in primary chondrocytes.Osteoarthritis and cartilage open · 2026Article
- Mapping gene expression across the microbiome-gut-brain axis of germ-free and specific pathogen-free mice.Microbiology (Reading, England) · 2026Article
- ACKR2 aids the regulation of bone marrow eosinophils to promote monocyte differentiation and anti-bacterial immunity.Nature communications · 2026Article
- TLR7-induced murine inflammation results in a global neuroinflammatory response driving neural circuit-specific transcriptomic changes.Scientific reports · 2026Article
- Chemokine receptor expression defines a trajectory from monocytes to mature macrophages in the lung.Journal of leukocyte biology · 2026Article
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- Activation of the Drosophila innate immune system accelerates growth in cooperation with oncogenic Ras.PLoS biology · 2025Article
- Exploring RNA-Seq Data Analysis Through Visualization Techniques and Tools: A Systematic Review of Opportunities and Limitations for Clinical Applications.Bioengineering (Basel, Switzerland) · 2025Review
- The distinctive signature of regulatory CD4 T cells committed in the human thymus.Frontiers in immunology · 2025Article
- Chronic inflammation degrades CD4 T cell immunity to prior vaccines in treated HIV infection.Nature communications · 2024Article
- Small extracellular vesicles derived from synovial fibroblasts contain distinct miRNA profiles and contribute to chondrocyte damage in osteoarthritis.Arthritis research & therapy · 2024Article
- CCR1 and CCR2 Coexpression on Monocytes Is Nonredundant and Delineates a Distinct Monocyte Subpopulation.Journal of immunology (Baltimore, Md. : 1950) · 2024Article
- Stratifying macrophages based on their infectious burden identifies novel host targets for intervention during Crohn's disease associated adherent-invasiveMicrobiology (Reading, England) · 2024Article
- Differences in transcriptional changes in psoriasis and psoriatic arthritis skin with immunoglobulin gene enrichment in psoriatic arthritis.Rheumatology (Oxford, England) · 2024Article
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- An intact S-layer is advantageous to Clostridioides difficile within the host.PLoS pathogens · 2023Article
- Cutaneous lesions in psoriatic arthritis are enriched in chemokine transcriptomic pathways.Arthritis research & therapy · 2023Article
- bulkAnalyseR: an accessible, interactive pipeline for analysing and sharing bulk multi-modal sequencing data.Briefings in bioinformatics · 2023Article
- PredPromoter-MF(2L): A Novel Approach of Promoter Prediction Based on Multi-source Feature Fusion and Deep Forest.Interdisciplinary sciences, computational life sciences · 2022Article
- Dissecting the molecular control of immune cell accumulation in the inflamed joint.JCI insight · 2022Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundOnce bulk RNA-seq data has been processed, i.e. aligned and then expression and differential tables generated, there remains the essential process where the biology is explored, visualized and interpreted. Without the use of a visualisation and interpretation pipeline this step can be time consuming and laborious, and is often completed using R. Though commercial visualisation and interpretation pipelines are comprehensive, freely available pipelines are currently more limited.
resultsHere we demonstrate Searchlight, a freely available bulk RNA-seq visualisation and interpretation pipeline. Searchlight provides: a comprehensive statistical and visual analysis, focusing on the global, pathway and single gene levels; compatibility with most differential experimental designs irrespective of organism or experimental complexity, via three workflows; reports; and support for downstream user modification of plots via user-friendly R-scripts and a Shiny app. We show that Searchlight offers greater automation than current best tools (VIPER and BioJupies). We demonstrate in a timed re-analysis study, that alongside a standard bulk RNA-seq processing pipeline, Searchlight can be used to complete bulk RNA-seq projects up to the point of manuscript quality figures, in under 3 h.
conclusionsCompared to a manual R based analysis or current best freely available pipelines (VIPER and BioJupies), Searchlight can reduce the time and effort needed to complete bulk RNA-seq projects to manuscript level. Searchlight is suitable for bioinformaticians, service providers and bench scientists. https://github.com/Searchlight2/Searchlight2 .
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