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This repository consists of the pipeline scripts associated with the research paper “Implementing flowDensity for Automated Analysis of Bone Marrow Lymphocyte Population” by Eskandari et al. (2020).
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The program analyzes flow cytometry data (.fcs) using flowDensity to automate analysis for evaluation of lymphocyte subsets in bone marrow biopsy specimens.
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Outline:
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The main directory is divided into three groups - data, scripts, and result.
- Data directory contains fcs files for different cell types such as T cells, B cells, and CD34 cells. User needs to manually add flow cytometry data in .fcs format for each cell type in data/{cell type}.
- Result directory contains the output of the program in respective cell type folder. Sequential gating and PCA visualization outputs are present in result/{cell type}. Comprehensive expression analysis outputs are present in result/{cell type}/Independent/.
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The pipeline consists of the following four steps -
- step 1: run flowDensity with optimized parameters with parental gating
- step 2: run flowDensity with optimized parameters for comprehensive expression analysis
- step 3: PCA visualization
- step 4: Comprehensive expression analysis visualization
[user@hpc scripts]$ bash runFlowDensityAnalysis.sh -t Tcells
Started processing cell type ...Tcells
Started processing sample ...Sample
step 1: run flowDensity with optimized parameters with parental gating
step 2: run flowDensity with optimized parameters for comprehensive expression analysis
step 3: PCA visualization
...processing PCA analysis...
...cell type is ...Tcells
...result files present in ../result/Tcells/
step 4: Comprehensive expression analysis visualization
...processing comprehensive expression analysis...
...cell type is ...Tcells
...result files present in ../result/Tcells/Independent/
Completed processing sample ...Sample
Completed processing cell type ...Tcells
- Result in ../result/Tcells/Independent/:
