PALMO (Platform for Analyzing Longitudinal Multi-omics data)
is a platform for anayzing longitudinal data from bulk as well as single cell. It allows to identify inter-, intra-donor variations in genes over longitudinal time points. The analysis can be done on bulk expression dataset without known celltype information or single cell with celltype/user-defined groups. It allows to infer stable and variable features in given donor and each celltype (or user defined group). The outlier analysis can be performed to identify techinical/biological perturbed samples in donor/participant. Further, differential analysis can be performed to deciher time-wise changes in gene expression in a celltype.
General workflow and analysis schema of PALMO. It can work with longitudinal data obtained from bulk such as clinical, bulk RNAseq, proteomic or single cell dataset from scRNAseq, and scATACseq.
To install library, simply run
library("devtools")
install_github("aifimmunology/PALMO")
library("PALMO")
There are couple of tutorials presented to help users to run PALMO on bulk and single cell data. The examples includes:
- Tutorial-1: Plasma proteome longitudinal data
- Tutorial-2: scRNA longitudinal data
- Tutorial-3: scATAC longitudinal data
- Tutorial-4: Multi-modal data integration
- Tutorial-5: CNP0001102 data (longitudinal COVID dataset)
- Tutorial-6: GSE129788 data (Mouse brain)
- Tutorial-7: Differential Gene analysis in longitudinal data
Suhas Vasaikar, Aarthi talla and Xiaojun Li designed the PALM algorithm. Suhas Vasaikar implemented the PALM package.
PALM is licensed under the MIT-License.