EasyOmics v1.2.0 Major Improvement of Whole App
December 30, 2024 major
This version beautify the layout of EasyOmics, explain the analysis ability of each function, and improve the analysis logic.
The container of EasyOmics is released on Docker Hub yuhan2000/EasyOmics.
Features:
- Display feedback for every step’s results on the screen.
- Add a homepage with the main graphic and logical connections between functions, referencing other Shiny software.
- Add a help interface linking to the menu of EasyOmics.
- Add a contact page to the menu of EasyOmics.
- Provide a textual explanation for all inputs and outputs for each function.
- Add generalized mixed linear model, linear regression model, and multi-loci mixed linear model.
- Additional visualization methods for multi-omics WAS.
- Integrate multi-omics QTL with multi-omics visualization.
- Consolidate results of different types of variations + standardize VCF formats.
- Enable customization of analysis parameters.
- Add time suffixes to all outputs.
Fixes:
- Modify text size for themes.
- Increase input restriction up to 300GB.
- Set feedback for warnings to red.
- Remove the display of results from the previous analysis.
- Handle parameter residues when switching between functions.
- Files are not removed to avoid long upload times.
- Process long phenotype strings for trait names.
EasyOmics v1.1.4 Function Robustness Improvement
July 14, 2024 major
This version improve the robustness of each function.
Features:
- Support result selection of SMR
- Add feedback message when running
Fixes:
- Change “vcf convert format” in Omic QTL function to enable more flexible data format.
- Enable character format p-value.
EasyOmics V1.0.0 First-Published
December 04, 2023 major
The publish version contain nine basic function for pupulation Omics data association analysis.
Features:
| Data Matching | Preparing input files for subsequent analysis. |
| Phenotype Analysis | Providing critical insights into the input data characteristics and facilitates the detection of outlier values. |
| GWAS | Testing the significance of associations between each SNP and the phenotype using a linear mixed model. |
| COJO | Fine mapping of GWAS result and identify secondary association signals. |
| Locus Zoom | Displaying the significance, linkage, and nearby genes of SNPs in specific chromosome regions. |
| Omic QTL | Employing linear models for association analysis of omics data and genotype data. |
| Two Traits MR | Exploring causal relationships between two traits. |
| SMR | Exploring causal relationships between trait and omic molecular trait. |
| OmicWAS | Testing the associations between omic data and complex traits. |