Package: ExpHunterSuite 1.21.0

James Perkins

ExpHunterSuite: Package for the Comprehensive Analysis of Transcriptomic Data

The ExpHunterSuite implements a comprehensive protocol for the analysis of transcriptional data using established R packages and combines their results. It covers key steps including differential expression analysis, co-expression analysis, and functional enrichment for RNA-seq data. The package provides interactive R functions as well as command-line scripts that wrap these functions.

Authors:James Perkins

ExpHunterSuite_1.21.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ExpHunterSuite/json (API)

# Install 'ExpHunterSuite' in R:

install.packages('ExpHunterSuite', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

degh_output - Output data from the main_degenes_Hunter function
target - Target data containing sample information for the toc data
toc - Table of counts dummy dataset for DEgeneHunter examples

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

geneexpressionworkflow

3.18 score 27 exports 304 dependencies

Last updated from:b351f29bbe. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.
A new build is currently in progress.

Target	Result	Time
bioc-checks	ERROR	403
linux-devel	WARNING	821
source / vignettes	OK	748
linux-release	WARNING	794
macos-release	WARNING	564
macos-oldrel	WARNING	462
windows-devel	WARNING	707
windows-release	WARNING	626
windows-oldrel	WARNING	625
wasm-release	OK	497

Exports:acc degsynth fmeasure get_org_db get_organism_table get_stats get_stats_from_cm install_DEgenes_hunter load_and_parse_gmt load_synth_dataset main_clusters_to_enrichment main_degenes_Hunter main_functional_hunter multienricher_gsea multienricher_ora multienricher_topGO parse_pseudocounts ppv recall rtable2measures spc target_generation write_clusters_to_enrichment write_df_list_as_tables write_enrich_files write_expression_report write_functional_report

Dependencies:abind aisdk AnnotationDbi AnnotationHub annotatr ape aplot arrangements askpass assertthat backports base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocVersion biomaRt Biostrings bit bit64 bitops blob boot broom BSgenome bslib ca cachem callr car carData caTools checkmate cigarillo cli clipr cluster clusterProfiler codetools colorspace contfrac cowplot cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray dendextend Deriv DESeq2 deSolve diffcoexp DiffCorr digest dir.expiry doBy doParallel DOSE dplyr DT dynamicTreeCut edgeR egg ellipse elliptic emmeans enrichit enrichplot estimability evaluate exactRankTests FactoInvestigate FactoMineR farver fastcluster fastmap fdrtool filelock flashClust fontawesome fontBitstreamVera fontLiberation fontquiver forcats foreach forecast foreign formatR Formula fracdiff fs futile.logger futile.options gclus gdtools generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggraph ggrepel ggridges ggtangle ggtree glmnet glue gmp GO.db GOSemSim GPArotation gplots graph graphite graphlayouts gridExtra gridGraphics gson gtable gtools haven heatmaply highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 hypergeo igraph impute IRanges irlba isoband iterators jomo jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r later lattice lazyeval leaps lifecycle limma lme4 lmtest locfit magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv mice miceadds mime minqa miRBaseVersions.db mitml mitools MKdescr MKinfer mnormt modelr multcompView multtest mvtnorm nlme nloptr nnet NOISeq numDeriv openssl ordinal otel pan patchwork pbkrtest pcaMethods permute pillar pkgconfig plotly plyr png polyclip preprocessCore prettyunits processx progress promises ps psych purrr qap quantreg qvalue R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl Rdpack reactome.db ReactomePA readr reformulas regioneR registry reshape2 restfulr Rhtslib rjson rlang rmarkdown ROCR rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors S7 sass scales scatterpie scatterplot3d Seqinfo seriation shape showtext showtextdb snow SparseArray SparseM statmod stringi stringr SummarizedExperiment survival sys sysfonts systemfonts tibble tidydr tidygraph tidyr tidyselect tidytree timeDate tinytex topGO treeio TSP tweenr txdbmaker tximport tzdb ucminf UCSC.utils urca utf8 vctrs vegan viridis viridisLite vroom webshot WGCNA withr xfun XML xml2 XVector yaml yulab.utils zoo

The Expression Hunter Suite

Version Info | Introduction | Differential Expression Analysis | More complex model designs. | Co-expression Analysis | Functional Analysis - Expression Data | Functional Analysis - general | Obtaining Reports | Functional Analysis - special options for reports | Command-line Package Usage | Usage | 1. Command line scripts for differential expression analysis. | Non-canonical usage scenarios: | A. Differential expression corrected by extra factors | B. Genes co-expression analysis with WGCNA | C. Analysing pre-normalized data with WGCNA | D. Using a pre-calculated list of DEA genes | E. Multifactorial (2x2) analysis to look for interactions between factors and effects in distinct groups | F. Multifactorial nested (2x2xn and 2xnxn) analysis to look for interactions between factors and effects in distinct groups where the groups contain paired samples (e.g. the same patient/control before and after treatment) | 2. Command line scripts for functional enrichment analysis. | DEgenes Hunter functional enrichment examples of use

Rendered fromhunter.Rmdusingknitr::rmarkdown

Last update: 2024-04-19
Started: 2020-12-18

Help page	Topics
Calculates accuracy from a measures dataframe	acc
Output data from the main_degenes_Hunter function	degh_output
Main function to generate synthetic data using an specific exponential distribution for logFC	degsynth
download kegg db for a given organism	download_latest_kegg_db
Extract value from confusion matrix	extract_from_cm
Custom function to generate exponentially degradated foldchange range	fcfunc
Calculates F measure from a measures dataframe	fmeasure
get path for KEGG db for downloading/usage	get_kegg_db_path
Obtain an org_db object from a current_organism_info, obtained from subsetting the results of get_organism_table()	get_org_db
Table with information abaut all organism available	get_organism_table
Function to calculate full set of measures from a confusion data frame	get_stats
Obtain full set of measures from a confusion matrix	get_stats_from_cm
Method used to import hidden functions legally for CRAN check	get_unexported_function
Function to generate scatter plot for each gene in a hunter table and show logFC per package taking into account the variablity between them	ht2logFCPlot
Hunter installation Function	install_DEgenes_hunter
Load a GMT format file and return a dataframe in correct format	load_and_parse_gmt
Loads Hunter DEG analysis table and simulated TRUE DEG vector. Concat in training/testing ML data frame format and returns it.	load_synth_dataset
Loads stored WGCNA results in DEgenes Hunter expression analysis package folder and returns in compact object	load_WGCNA_results
Perform enrichment analysis on multiple lists of genes	main_clusters_to_enrichment
Main DEgenes Hunter Function	main_degenes_Hunter
Perform Functional analysis with different enrichment corpora.	main_functional_hunter
Perform gsea enrichment analysis of a list of genes	multienricher_gsea
Perform ORA enrichment analysis of a list of genes	multienricher_ora
Perform topGO enrichment analysis of a list of genes	multienricher_topGO
Parallelize function execution in list with multiple elements	parallel_list
main_parse_pseudocounts Functions that loads pseudommappers results and complite it into a table of counts	parse_pseudocounts
Calculates Positive Predictive Value from a measures dataframe	ppv
Calculates Recall from a measures dataframe	recall
Calculates emasures from result tables	rtable2measures
Scale a matrix using minimum-maximum method	scale_data_matrix
Funtion used to scale a vector of numeric values from (x_min,x_max) range to (y_min,y_max) range. f : R -> R (x_min, x_max) -> (y_min, y_max) vect - x_min f(vect,y_min,y_max) = ----- x (y_max - y_min) + y_min x_max - x_min	scale_range
Calculates specificity from a measures dataframe	spc
Function to Simulate Treatment-Control paired experiments for genes expression count tables. Pipeline inspired on TCC simulateReadCounts function	STC
Target data containing sample information for the toc data	target
Function to generate targets file Load target file if it exists, otherwise use the -C and -T flags. Note target takes precedence over target.	target_generation
Table of counts dummy dataset for DEgeneHunter examples	toc
Translates a given gene ID using a dictionary. Note: one unknown ID can corresponds to many known ids.	translate_from_table
if pairwise_termsim throws an error, remove dup cat descriptions Only seems to be a problem with Reactome - to study further Further investigation re: number of cats also required	trycatch_pairwise_termsim
Write Main clusters to enrichment output This function allows you to report the Functional analysis.	write_clusters_to_enrichment
Function to write expression package results. Write to disk the results of each diff expression package	write_df_list_as_tables
Write enrichment files related to functional_hunter results list	write_enrich_files
Write Main DEgenes Hunter report	write_expression_report
Write Main DEgenes Hunter functional report This function allows you to report the Functional analysis.	write_functional_report

Package: ExpHunterSuite 1.21.0

ExpHunterSuite: Package for the Comprehensive Analysis of Transcriptomic Data

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