ArticleBMC bioinformatics2021
SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses.
Article in BMC bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 18 papers.
What it found
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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.
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Who cites it
18 citing papers in PubMed, 28 citations in OpenAlex.
- Molecular impact of nicotine and smoking exposure on the developing and adult mouse brain.Addiction neuroscience · 2026Article
- Transcriptional Response to Chronic Long-Access Fentanyl Self-Administration in Rat Habenula and Amygdala.Addiction biology · 2026Article
- Fine mapping of PTSD GWAS reveals a role for amygdalabioRxiv : the preprint server for biology · 2026Article
- Transcriptional response to chronic long-access fentanyl self-administration in rat habenula and amygdala.bioRxiv : the preprint server for biology · 2025Article
- Transcriptomic Analysis of the Human Habenula in Schizophrenia.The American journal of psychiatry · 2025Article
- Lewy body dementia promotion by air pollutants.Science (New York, N.Y.) · 2025Article
- RnaXtract, a tool for extracting gene expression, variants, and cell-type composition from bulk RNA sequencing.Scientific reports · 2025Article
- Benchmark of cellular deconvolution methods using a multi-assay dataset from postmortem human prefrontal cortex.Genome biology · 2025Article
- 3t-seq: automatic gene expression analysis of single-copy genes, transposable elements, and tRNAs from RNA-seq data.Briefings in bioinformatics · 2024Article
- Systems biology dissection of PTSD and MDD across brain regions, cell types, and blood.Science (New York, N.Y.) · 2024Article
- Sex affects transcriptional associations with schizophrenia across the dorsolateral prefrontal cortex, hippocampus, and caudate nucleus.Nature communications · 2024Article
- Comparison of gene expression in living and postmortem human brain.medRxiv : the preprint server for health sciences · 2023Article
- BiocMAP: a Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data.BMC bioinformatics · 2023Article
- Prioritization of potential causative genes for schizophrenia in placenta.Nature communications · 2023Article
- Article
- Genetics and Brain Transcriptomics of Completed Suicide.The American journal of psychiatry · 2022Article
- Genome-wide sequencing-based identification of methylation quantitative trait loci and their role in schizophrenia risk.Nature communications · 2021Article
- Correction to: SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor‑powered RNA‑seq analyses.BMC bioinformatics · 2021Article
Corrections and comments
- Erratum issued
Authors and funding
12 authors at 6 institutions in 2 countries.
Funding
Abstract
backgroundRNA sequencing (RNA-seq) is a common and widespread biological assay, and an increasing amount of data is generated with it. In practice, there are a large number of individual steps a researcher must perform before raw RNA-seq reads yield directly valuable information, such as differential gene expression data. Existing software tools are typically specialized, only performing one step-such as alignment of reads to a reference genome-of a larger workflow. The demand for a more comprehensive and reproducible workflow has led to the production of a number of publicly available RNA-seq pipelines. However, we have found that most require computational expertise to set up or share among several users, are not actively maintained, or lack features we have found to be important in our own analyses.
resultsIn response to these concerns, we have developed a Scalable Pipeline for Expression Analysis and Quantification (SPEAQeasy), which is easy to install and share, and provides a bridge towards R/Bioconductor downstream analysis solutions. SPEAQeasy is portable across computational frameworks (SGE, SLURM, local, docker integration) and different configuration files are provided ( http://research.libd.org/SPEAQeasy/ ).
conclusionsSPEAQeasy is user-friendly and lowers the computational-domain entry barrier for biologists and clinicians to RNA-seq data processing as the main input file is a table with sample names and their corresponding FASTQ files. The goal is to provide a flexible pipeline that is immediately usable by researchers, regardless of their technical background or computing environment.
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.