ArticleCurrent protocols in bioinformatics2017
Data Analysis Pipeline for RNA-seq Experiments: From Differential Expression to Cryptic Splicing.
Article in Current protocols in bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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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.
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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
29 citing papers in PubMed.
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- The Ability of a 3-Gene Host Signature in Blood to Distinguish Tuberculous Meningitis From Other Brain Infections.The Journal of infectious diseases · 2024Article
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- Alternative polyadenylation alters protein dosage by switching between intronic and 3'UTR sites.Science advances · 2023Article
- Cell-type deconvolution of bulk RNA-Seq from kidney using opensource bioinformatic tools.bioRxiv : the preprint server for biology · 2023Article
- Exploration of prognosis and immunometabolism landscapes in ER+ breast cancer based on a novel lipid metabolism-related signature.Frontiers in immunology · 2023Article
- Expression and Functional Studies of Leaf, Floral, and Fruit Developmental Genes in Non-model Species.Methods in molecular biology (Clifton, N.J.) · 2023Article
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- Interpretation of network-based integration from multi-omics longitudinal data.Nucleic acids research · 2022Article
- Computational analyses of mechanism of action (MoA): data, methods and integration.RSC chemical biology · 2022Review
- Targeting Asparagine and Serine Metabolism in Germinal Centre-Derived B Cells Non-Hodgkin Lymphomas (B-NHL).Cells · 2021Article
- Inhibition of the lncRNA Coded within Transglutaminase 2 Gene Impacts Several Relevant Networks in MCF-7 Breast Cancer Cells.Non-coding RNA · 2021Article
- Regulation of telomere homeostasis and genomic stability in cancer byScience advances · 2021Article
- Regeneration of the pulmonary vascular endothelium after viral pneumonia requires COUP-TF2.Science advances · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
RNA sequencing (RNA-seq) is a high-throughput technology that provides unique insights into the transcriptome. It has a wide variety of applications in quantifying genes/isoforms and in detecting non-coding RNA, alternative splicing, and splice junctions. It is extremely important to comprehend the entire transcriptome for a thorough understanding of the cellular system. Several RNA-seq analysis pipelines have been proposed to date. However, no single analysis pipeline can capture dynamics of the entire transcriptome. Here, we compile and present a robust and commonly used analytical pipeline covering the entire spectrum of transcriptome analysis, including quality checks, alignment of reads, differential gene/transcript expression analysis, discovery of cryptic splicing events, and visualization. Challenges, critical parameters, and possible downstream functional analysis pipelines associated with each step are highlighted and discussed. This unit provides a comprehensive understanding of state-of-the-art RNA-seq analysis pipeline and a greater understanding of the transcriptome. © 2017 by John Wiley & Sons, Inc.
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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.