DESCRIPTION

Package: hpgltools
Type: Package
Title: A pile of (hopefully) useful R functions
Version: 1.0
Date: 2018-03-01
Author: Ashton Trey Belew, Keith Hughitt
Authors@R: c(person("Ashton", "Belew", email="abelew@gmail.com", role=c("aut","cre")),
             person("Keith", "Hughitt", email="khughitt@umd.edu", role=c("aut")),
             person("Jerry", "Zhao", email="zhaojerry123@gmail.com", role=c("aut")))
Maintainer: Ashton Trey Belew <abelew@gmail.com>
Description: This is a set of functions I have been using in my various analyses
             in the El-Sayed laboratory. The set of tasks included herein run a
             spectrum from preprocessing count-tables from RNAseq-like data,
             through differential expression analyses, to post-processing tasks
             like gene ontology enrichment.  Along the way, these function seek
             to make plotting analyses consistent, provide multiple entry-points
             to the various tools, and handle corner cases which are not
             flexibly handled by the packages this is based upon.
License: GPL-2 | file LICENSE
Suggests:
  affy, AnnotationDbi, AnnotationForge, AnnotationHub, ape,
  BiocGenerics, BiocManager, biomaRt, Biostrings, bluster, broom,
  BRAIN, BSgenome,
  caret, Category, cleaver, clusterProfiler, corpcor, corrplot, curl,
  DALEX, DBI, DEGreport, desc, DESeq2, devEMF, devtools, digest, directlabels,
  doParallel, dorothea, doSNOW, dotwhisker, DSS,
  EBSeq, EDASeq, edgeR, enrichplot, 
  fastcluster, fastICA, ffpe, fission, flashClust,
  genefilter, GenomicRanges, GenomeInfoDb, genoPlotR, ggdendro,
  ggrepel, ggsankey, ggstatsplot, ggthemes, goseq, GO.db, GOstats,
  graph, GSVA, GSVAdata, gtools, gplots, gProfileR, gprofiler2,
  Heatplus, Hmisc, Homo.sapiens, htmlwidgets, hpgldata, httr,
  iDA, igraph, IHW, inflection, IRanges, isva, iterators,
  jsonlite,
  KEGGREST, KEGGgraph, kmer,
  lattice, limma, locfit, lubridate,
  MatrixGenerics, matrixStats, miscTools, motifRG, MSnbase, mygene, mzR,
  networkD3, NOISeq, numform,
  openxlsx, OrganismDbi,
  pander, parallel, pasilla, pathfindR, pathview, pcaMethods, Peptides,
  pheatmap, plyr, preprocessCore, pROC, PROPER, purrr,
  qvalue,
  R.utils, RColorBrewer, RCurl, readr, reactome.db, ReactomePA, readODS, readxl,
  reshape2, rGADEM, Rgraphviz, rhdf5, Rhdf5lib, rjson, rmarkdown, robust,
  robustbase, Rsamtools, Rtsne,
  rtracklayer, ruv, RUVSeq, rvest,
  scales, Seurat, seqLogo, skimr, SmartSVA, spgs, statmod, stringi,
  stringr, SWATH2stats,
  taxize, testthat, tibble, tidyr, tidymodels, tidyselect, topGO, tximport,
  UniProt.ws, UpSetR, uwot, webp,
  varhandle, variancePartition, Vennerable,
  WGCNA,
  xCell, xml2
Imports:
  data.table, DOSE, dplyr,
  forcats, foreach,
  GenomicFeatures, ggplot2, glue, GSEABase,
  IRanges,
  knitr,
  magrittr, methods,
  plotly,
  rlang, RSQLite,
  shiny, sva,
  tidyselect,
  varhandle, variancePartition
Depends:
  Biobase, SummarizedExperiment, S4Vectors, glue, Matrix
VignetteBuilder: knitr
ByteCompile: true
biocViews: DifferentialExpression
Encoding: UTF-8
RoxygenNote: 7.3.1
Collate:
  '01_hpgltools.R'
  'alt_splicing.R'
  'annotation_biomart.R'
  'annotation_genbank.R'
  'annotation_gff.R'
  'annotation_kegg.R'
  'annotation_microbesonline.R'
  'annotation_orgdb.R'
  'annotation_txt.R'
  'annotation_uniprot.R'
  'annotation_shared.R'
  'classify.R'
  'de_shared.R'
  'de_basic.R'
  'de_edger.R'
  'de_deseq.R'
  'de_ebseq.R'
  'de_limma.R'
  'de_noiseq.R'
  'de_plots.R'
  'de_xlsx.R'
  'de_varpart.R'
  'dimension_reduction.R'
  'expt.R'
  'gene_sets.R'
  'gsva.R'
  'helpers_misc.R'
  'metadata.R'
  'model_testing.R'
  'model_varpartition.R'
  'motif.R'
  'network.R'
  'normalize_shared.R'
  'normalize_filter.R'
  'normalize_convert.R'
  'normalize_transform.R'
  'normalize_norm.R'
  'normalize_batch.R'
  'ontology_shared.R'
  'ontology_goseq.R'
  'ontology_gprofiler.R'
  'ontology_gostats.R'
  'ontology_topgo.R'
  'ontology_clusterprofiler.R'
  'ontology_plots.R'
  'ontology_xlsx.R'
  'ontology_kegg.R'
  'pcr.R'
  'peptides.R'
  'phylo.R'
  'plot_shared.R'
  'plot_bar.R'
  'plot_distribution.R'
  'plot_dotplot.R'
  'plot_heatmap.R'
  'plot_hist.R'
  'plot_point.R'
  'plot_proteomics.R'
  'plot_venn.R'
  'plot_circos.R'
  'plot_genplot.R'
  'plot_misc.R'
  'power_estimation.R'
  'proteomics.R'
  'se.R'
  'sequence.R'
  'shiny.R'
  'singlecell.R'
  'tf.R'
  'tnseq.R'
  'variants.R'
  'xlsx.R'
  'zzz_methods.R'
  'zzz_print.R'
  'zzz_subset.R'