DESCRIPTION

Package: arseq
Type: Package
Title: Automated RNA Sequencing Analysis Pipeline
Version: 2.3.2
Author: Ajit Johnson Nirmal
Maintainer: Ajit Johnson Nirmal <ajitjohnson.n@gmail.com>
Description: Biologist friendly program that supports the following analysis in an automated fashion with minimal coding requirement. 
    Currently supported Model Organism: Human.
    Over all data structure: 
    Euclidean distance between samples.
    Poisson distance between samples.
    Principal component analysis.
    Principal component analysis Eigenvectors.
    Multidimensional scaling analysis and most variable genes.
    Between groups of interest:
    Differential gene expression analysis using 'DESeq2'.
    Volcano plot of differentially expressed genes.
    Euclidean distance between samples.
    Poisson distance between samples.
    Principal component analysis.
    Principal component analysis Eigenvectors.
    Multidimensional scaling analysis.
    Gene Ontology enrichment of the differentially expressed genes.
    Kyoto Encyclopedia of Genes and Genomes pathway enrichment of the differentially expressed genes.
    Kyoto Encyclopedia of Genes and Genomes pathway diagrams of the top 5 enriched pathways. 
    Gene Set Enrichment Analysis (H, C1, C2, C3, C4, C5, C6, C7 gene set).
    Reactome Enrichment Analysis
    Custom Gene Set Enrichment Analysis.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends:
  R (>= 3.4.0)
biocViews:
Imports:
  GenomeInfoDb (>= 1.12.0),
  GenomeInfoDbData (>= 0.1.0),
  geneLenDataBase (>= 1.9.2),
  DESeq2 (>= 1.22),
  goseq (>= 1.34),
  plyr (>= 1.8),
  dplyr (>= 0.8),
  ggplot2 (>= 3.2),
  gridExtra (>= 2.3),
  stringr (>= 1.4),
  KEGGREST (>= 1.22),
  fgsea (>= 1.8),
  msigdbr (>= 6.2),
  biomaRt (>= 2.38),
  RColorBrewer (>= 1.1),
  pheatmap (>= 1.0),
  viridis (>= 0.5),
  PoiClaClu (>= 1.0),
  ggrepel (>= 0.8),
  grid (>= 3.5),
  gplots (>= 3.0),
  EnhancedVolcano (>= 1.0),
  pathview (>= 1.22),
  gage (>= 2.32),
  AnnotationDbi (>= 1.44),
  matrixStats (>= 0.54.0),
  circlize (>= 0.4.9),
  ComplexHeatmap (>= 2.5.2),
  clusterProfiler (>= 3.14.3),
  ReactomePA (>= 1.30.0),
  HiClimR (>= 2.1.5)
RoxygenNote: 7.1.1
URL: https://github.com/ajitjohnson/arseq
Suggests: testthat