ArticleBioinformatics (Oxford, England)2025
SpectroPipeR-a streamlining post Spectronaut® DIA-MS data analysis R package.
Article in Bioinformatics (Oxford, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
10 citing papers in PubMed.
- Immunoglobulin sub-class levels define inter-donor plasma variability: a longitudinal dual-lab study.Molecular systems biology · 2026Article
- What Does Next-Generation Mass Spectrometry Offer for Proteomics? A Comprehensive Platform Comparison.Journal of proteome research · 2026Article
- IL-4/STAT6-signaling Influences Local Inflammation and Regeneration Processes During Acute Pancreatitis and Promotes Fibrosis by a Direct Activation of Pancreatic Fibroblasts During Chronic Pancreatitis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Unraveling proteomic chaos by independent component analysis-ClpX proficiency promotes the iron and oxygen limitation responses ofmSystems · 2025Article
- Linking Virulence and Iron Limitation Response inJournal of proteome research · 2025Article
- The ClpXP protease and the ClpX unfoldase control virulence, cell division, and autolysis inMicrobiology spectrum · 2025Article
- Integrated genomic and proteomic analysis of the mouse-adaptedCurrent research in microbial sciences · 2025Article
- Requirement of ClpX for CtsR dissociation from its operator elements upon heat stress inFrontiers in microbiology · 2025Article
- The global proteome ofFrontiers in cellular and infection microbiology · 2025Article
- Global quantitative proteome analysis of a multi-resistantFrontiers in microbiology · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
Abstract
summaryProteome studies frequently encounter challenges in down-stream data analysis due to limited bioinformatics resources, rapid data generation, and variations in analytical methods. To address these issues, we developed SpectroPipeR, an R package designed to streamline data analysis tasks and provide a comprehensive, standardized pipeline for Spectronaut® DIA-MS data. This novel package automates various analytical processes, including XIC plots, ID rate summary, normalization, batch and covariate adjustment, relative protein quantification, multivariate analysis, and statistical analysis, while generating interactive HTML reports for e.g. ELN systems. AVAILABILITY AND IMPLEMENTATION: The SpectroPipeR package (manual: https://stemicha.github.io/SpectroPipeR/) was written in R and is freely available on GitHub (https://github.com/stemicha/SpectroPipeR).
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.