DGRPy is a python package for DGRP microbiome data analysis
What DGRPy will/can do?
- Load OTU, Taxonomy data from different DGRP based studies
- Load sample metadata from different DGRP based studies.
- Load DGRP variation data for mGWAS study.
- Load taxonomic database files of Greengeens, SILVA, NCBI, OTT or RDP.
- Combine,filter, manipulate OTU tables or samples based on various criteria
- Combined OTUs based on taxonomy ranks
- Filter OTUs with taxonomic lineages that only present in one of loaded taxonomic databases.
- Associate OTU ids of loaded OTU data with any of the given databases
- Remove OTUs based on cutoff values
- Remove specific OTUs
- Generate separate OTU frame with present/absent data
- Generate phylogenetic trees
- Available OTUs taxa using any of taxonomic database files
- Generate phylogenetic trees based OTU taxa with reduced ranks
- Form groups of
- Samples based on sample metadata
- Samples based on clustering data
- OTUs based on taxonomic ranks
- Normalize or Denormalize OTU reads
- Calculate various Alpha and Beta diversities measurements.
- Perform required data analysis in Python or via R
- Perform mGWAS via Plink (or if possible directly in DGRPy) and load all data to DGRPy
- Only after final OTU data is ready! Initialize required data analysis plan(s). Though each plan must contain following information, some can share plans
- Sample and OTU taxa groupings
- List of desired alpha and beta diversity measurements
- List of data analysis methods that must be performed such as MDS, clustering, etc.
- List of required plots such as Screeplots, 2D or 3D PCoA plots, boxplots, heatmaps, abundance plots, etc.
- List of required tables, summaries, etc.
- Generate Reports. Following must be specifie
- Report format, HTML, PDF, etc.
- Excel outputs
- Separate report generation for each plan?
Farid MUSA (mmtechslv@gmail.com)
- Project is under early development stage
- Any contribution, recommendation or remark is welcome
- Feel free to contact me