CRAN/E | PALMO

PALMO

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

Installation

About

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.

github.com/aifimmunology/PALMO
Bug report File report

Key Metrics

Version 0.1.2
R ≥ 4.0
Published 2022-08-17 612 days ago
Needs compilation? no
License MIT
License File
CRAN checks PALMO results

Downloads

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Last 90 days 129 +54%
Last 365 days 685 -72%

Maintainer

Maintainer

Suhas Vasaikar

suhas.vasaikar@alleninstitute.org

Authors

Suhas Vasaikar

aut / cre

Aarthi Talla

aut / ctb

Xiaojun Li

aut / ctb

Material

NEWS
Reference manual
Package source

Vignettes

PALMO

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

PALMO archive

Depends

R ≥ 4.0
methods
grid
graphics
stats
grDevices

Imports

Seurat ≥ 3.9
ggrepel ≥ 0.9
pbapply ≥ 1.4
lme4 ≥1.1
ggforce ≥ 0.3
MAST ≥ 1.14
factoextra ≥ 1.0
Rtsne ≥ 0.15
knitr ≥ 1.30
dplyr
ggplot2
reshape2
ComplexHeatmap
circlize
cowplot
pheatmap
tidyverse
utils

Suggests

ggpubr
rmarkdown