R (>= 4.0.0), jsonlite, rmarkdown, gdata, openssl, Biobase
roxygen2 (>= 3.1.0), testthat,usethis,knitr, XLConnect, xlsx,
openxlsx

R (>= 4.0.0), jsonlite, rmarkdown, openssl, utils, Biobase
roxygen2 (>= 3.1.0), testthat,usethis,knitr,
WriteXLS,XLConnect,openxlsx,xlsx, officedown

Discriminant Analysis for Evolutionary Inference
Discriminant Analysis (DA) for evolutionary inference (Qin, X. et al, 2020, <doi:10.22541/au.159256808.83862168>), especially for population genetic structure and community structure inference. This package incorporates the commonly used linear and non-linear, local and global supervised learning approaches (discriminant analysis), including Linear Discriminant Analysis of Kernel Principal Components (LDAKPC), Local (Fisher) Linear Discriminant Analysis (LFDA), Local (Fisher) Discriminant Analysis of Kernel Principal Components (LFDAKPC) and Kernel Local (Fisher) Discriminant Analysis (KLFDA). These discriminant analyses can be used to do ecological and evolutionary inference, including demography inference, species identification, and population/community structure inference.
c(person("Xinghu", "Qin", role=c("aut", "cre", "cph"),
email="qinxinghu@gmail.com", comment=c(ORCID="0000-0003-2351-3610")))
BiomedicalInformatics, ChIPSeq, Clustering, Coverage,
DNAMethylation, DifferentialExpression,
DifferentialMethylation,Software, DifferentialSplicing,
Epigenetics, FunctionalGenomics, GeneExpression,
GeneSetEnrichment, Genetics, ImmunoOncology,
MultipleComparison, Normalization, Pathways, QualityControl,
RNASeq, Regression, SAGE, Sequencing, Software, SystemsBiology,
TimeCourse, Transcription, Transcriptomics

Dimensionality Assessment using Minimum Rank Factor Analysis
Performs Parallel Analysis for assessing the dimensionality of a set of variables using Minimum Rank Factor Analysis (see Timmerman & Lorenzo-Seva (2011) <DOI:10.1037/a0023353> and ten Berge & Kiers (1991) <DOI:10.1007/BF02294464> for more information).
The package also includes the option to compute Minimum Rank Factor Analysis by itself, as well as the Greater Lower Bound calculation.