sesamestr
Automated Pipeline to run SeSAMe Analysis on MM285 Methylation Array
Science Score: 57.0%
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✓CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
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✓DOI references
Found 2 DOI reference(s) in README -
○Academic publication links
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.6%) to scientific vocabulary
Repository
Automated Pipeline to run SeSAMe Analysis on MM285 Methylation Array
Basic Info
- Host: GitHub
- Owner: Stefanos-Apostle
- Language: R
- Default Branch: main
- Size: 860 KB
Statistics
- Stars: 3
- Watchers: 1
- Forks: 1
- Open Issues: 2
- Releases: 2
Metadata Files
README.md
SeSAMeStr Pipeline workflow. (A) Function and input requirements to run the pipeline. (B) Output directory structure with populated results. (C) Key QC figures generated in the preprocessing step (Detection rate, SNP allele frequency heatmap, Red-Green QQ Plot, Intensity Plot). (D) Figures generated during the PCA analysis based on input formula. (E) Key figures generated from DML analysis step based on input formula (Volcano plot, heatmap of significant CpG’s, GO Enrichment, Test Set Enrichment).
SeSAMeStr
This pipeline is meant to act as a first pass analysis of DNA CpG Methylation using the SeSAMe R-Package. This will take care of Quality Control, PCA, and Basic DML analysis. All files and plots will be output to output directory for ease of loading data back into R for either rerunning, replotting, or continuation of downstream analysis.
Step 1: Install SeSAMeStr R-Package from Github
library(devtools)
devtools::install_github("Stefanos-Apostle/SeSAMeStr")
library(SeSAMeStr)
Step 2: Fill out the SeSAMeSTREETSample_Sheet
Download from Github
wget https://github.com/Stefanos-Apostle/SeSAMeStr/blob/main/SeSAMe_STREET_Sample_Sheet.xlsx
Step 3: Create the Output directory Architecture
.
├── DML
│ ├── DMR_Analysis
│ ├── GO_Enrichment
│ ├── Heatmaps
│ ├── testEnrichments
│ │ └──custom_sets
│ └── Volcano_plots
├── DimRed
└── QC
Step 4: Run the SeSAMe_STREET() Function
SeSAMeStr(Idat_dir = "path_to/Idat_dir",
out_dir = "path_to/output",
sample_sheet = "path_to/SeSAMe_STREET_Sample_Sheet.xlsx",
prep = "TQCDPB",
formula = ~ Condition1 + Condition2 + ...,
subsample = NA,
cores = 4)
Future Work
This has been built primarily for the MM285 platform, but is prepared to be extended to other platforms as well. This will happen if a personal/lab project requires it or if there is of interest by others in this extension.
Cite
Cite SeSAMeStr v1.0.0 by;
Apostle, S., Fagnocchi, L., & Pospisilik, J. A. (2023). SeSAMeStr: An Automated Pipeline for SeSAMe Methylation Array Analysis (Version 1.0.0) [Computer software]. https://doi.org/10.5281/zenodo.7510575
Owner
- Name: Stefanos Apostle
- Login: Stefanos-Apostle
- Kind: user
- Location: Grand Rapids, MI
- Company: Van Andel Institute
- Website: https://www.linkedin.com/in/stefanos-apostle-003a06104/
- Repositories: 2
- Profile: https://github.com/Stefanos-Apostle
Computational Biologist https://pospisiliklab.vai.org/
Citation (CITATION.cff)
cff-version: 1.2.0 message: "If you use this software, please cite it as below." authors: - family-names: "Apostle" given-names: "Stefanos" orcid: "https://orcid.org/0000-0001-7257-7421" - family-names: "Fagnocchi" given-names: "Luca" orcid: "https://orcid.org/0000-0002-9551-5474" - family-names: "Pospisilik" given-names: "J. Andrew" orcid: "https://orcid.org/0000-0002-9745-0977" title: "SeSAMeStr: An Automated Pipeline for SeSAMe Methylation Array Analysis" version: 1.0.0 doi: 10.5281/zenodo.7510575 date-released: 2023-01-06 url: "https://github.com/Stefanos-Apostle/SeSAMeStr"