Learn R Programming

PALMO (version 0.1.2)

Identify Intra and Inter-Donor Variations in Bulk or Single Cell Longitudinal Dataset

Description

It is a platform for analyzing longitudinal data from bulk as well as single cell datasets. It allows to identify variations in molecular features within and across donors over longitudinal time points. The analysis can be done on bulk expression dataset without known cell type information or single cell with cell type/user-defined groups. It allows to infer stable and variable features in given donor and each cell type (or user defined group). The outlier analysis can be performed to identify technical/biological perturbed samples in donor/participant. Further, differential analysis can be performed to decipher time-wise changes in gene expression in a cell type.

Copy Link

Version

Install

install.packages('PALMO')

Monthly Downloads

9

Version

0.1.2

License

MIT + file LICENSE

Issues

Pull Requests

Stars

Forks

Maintainer

Suhas Vasaikar

Last Published

August 17th, 2022

Functions in PALMO (0.1.2)

cvCalcBulkProfile

cvCalcBulkProfile Function
cvCalcSC

cvCalcSC Function
cvCalcSCProfile

cvCalcSCProfile Function
cvSCsampleprofile

cvSCsampleprofile Function
sample_correlation

sample_correlation Function
sclongitudinalDEG

sclongitudinalDEG Function
annotateMetadata

annotateMetadata Function
StableFeatures

StableFeatures Function
avgExpCalc

avgExpCalc Function
VarFeatures

VarFeatures Function
dimUMAPPlot

dimUMAPPlot Function
longitudinalmfuzz

longitudinalmfuzz Function
gene_featureplot

gene_featureplot Function
checkReplicates

checkReplicates Function
mergePALMOdata

mergePALMOdata Function
outlierDetect

outlierDetect Function
createPALMOfromsinglecellmatrix

createPALMOfromsinglecellmatrix Function
outlierDetectP

outlierDetectP Function
genecircosPlot

genecircosPlot Function
lmeVariance

lmeVariance Function
p_value_for_event

p_value_for_event Function
palmo-class

palmo class
createPALMOobject

createPALMOobject Function
cvCalcBulk

cvCalcBulk Function
multimodalView

multimodalView Function
naFilter

naFilter Function
variancefeaturePlot

variancefeaturePlot Function