xPore Postprocessing Visualization Code (Quarto)
This Quarto Markdown file contains a step-by-step workflow for analyzing xPore RNA modification data. It includes filtering, statistical analysis, and visualization to identify and explore differences in RNA modifications between samples. The outputs include:
- PCA plots to check sample clustering
- k-mer counts to see sequence patterns
- Volcano plots to show significant changes
- Heatmaps of modification levels
- Other visual summaries to help interpret the results
This workflow makes it easy to process and understand RNA modification data from nanopore sequencing.
SEEK ID: https://fairdomhub.org/data_files/7760?version=3
Filename:
Postprocessing_no_cov_filter.qmd
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Size: 128 KB
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Created: 8th Apr 2025 at 14:08
Last updated: 19th Dec 2025 at 13:01
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Version 3 (latest) Created 7th May 2025 at 14:46 by Ayat Ismail
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Version 2 Created 24th Apr 2025 at 08:08 by Ayat Ismail
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Version 1 (earliest) Created 8th Apr 2025 at 14:08 by Ayat Ismail
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Projects: Group Data Science, Methylation differences during respiratory infection, Implementation of Nanopore Sequencing for Detection of Treatment Induced Transcriptomic and Epitranscriptomic Changes in Leukaemic Tumour Models, OMICS of vascular smooth muscle cells under oxidative stress, Systems genetics of lung health and asthma (GWAS, PGS, QTL)
Institutions: Forschungszentrum Borstel
The FZB is the lung research center of the Leibniz Association and is therefore committed to the motto “theoria cum praxi”.
The FZB sees its scientific and socio-political task in basic, disease- and patient-oriented lung research and training in this field. The field of research includes chronic inflammatory diseases of the lung of infectious and non-infectious environmental and behavioral origin. Research focuses on tuberculosis, infections with non-tuberculous mycobacteria and other bacterial ...
Projects: Group Data Science, Group Microbial Interface Biology, Core Facility Fluorescence Cytometry, Targeting the immunoproteasome: Analyzing the biological effects of specific versus pan inhibition, Macrophage and neutrophil redox proteome in infection with Mycobacterium tuberculosis, Methylation differences during respiratory infection, Lipid droplet formation and dynamics in murine macrophages, OMICS of vascular smooth muscle cells under oxidative stress, Systems genetics of lung health and asthma (GWAS, PGS, QTL), Archaean stimulation of human primary PBMCs and PBMCs monocytes
Web page: https://fz-borstel.de
Programme: Research Center Borstel
Public web page: Not specified
Submitter: Ayat Ismail
Investigation: ONT direct RNA Sequencing
Assays: Comprehensive RNA Modification Analysis and Visualization
Majority direction kmer data files were used for the analysis. e.g: results/analysed_icg/xpore_cdna.all/diffmod_s1-s2/majority_direction_kmer_diffmod.table. which has been renamed to : s1_s2.table as uploaded here.
Submitter: Ayat Ismail
Biological problem addressed: Model Analysis Type
Investigation: ONT direct RNA Sequencing
Study: RNA modification detection
