Package: genekitr 1.2.8

Yunze Liu

genekitr: Gene Analysis Toolkit

Provides features for searching, converting, analyzing, plotting, and exporting data effortlessly by inputting feature IDs. Enables easy retrieval of feature information, conversion of ID types, gene enrichment analysis, publication-level figures, group interaction plotting, and result export in one Excel file for seamless sharing and communication.

Authors:Yunze Liu [aut, cre]

genekitr_1.2.8.tar.gz
genekitr_1.2.8.zip(r-4.5)genekitr_1.2.8.zip(r-4.4)genekitr_1.2.8.zip(r-4.3)
genekitr_1.2.8.tgz(r-4.4-any)genekitr_1.2.8.tgz(r-4.3-any)
genekitr_1.2.8.tar.gz(r-4.5-noble)genekitr_1.2.8.tar.gz(r-4.4-noble)
genekitr_1.2.8.tgz(r-4.4-emscripten)genekitr_1.2.8.tgz(r-4.3-emscripten)
genekitr.pdf |genekitr.html✨
genekitr/json (API)

# Install 'genekitr' in R:

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

Bug tracker:https://github.com/ganglilab/genekitr/issues

Datasets:

biocOrg_name - Datasets geneList entrez gene list with decreasing fold change value
deg - Datasets geneList entrez gene list with decreasing fold change value
ensOrg_name - Datasets geneList entrez gene list with decreasing fold change value
geneList - Datasets geneList entrez gene list with decreasing fold change value
hsapiens_probe_platform - Datasets geneList entrez gene list with decreasing fold change value
keggOrg_name - Datasets geneList entrez gene list with decreasing fold change value
msig_category - Datasets geneList entrez gene list with decreasing fold change value
msig_org - Datasets geneList entrez gene list with decreasing fold change value

On CRAN:

enrichment-analysis gene id-converter plotting

19 exports 53 stars 3.32 score 135 dependencies 1 dependents 19 scripts 1.5k downloads

Last updated 8 days agofrom:4db543377c. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 10 2024
R-4.5-win	OK	Sep 10 2024
R-4.5-linux	OK	Sep 10 2024
R-4.4-win	OK	Sep 10 2024
R-4.4-mac	OK	Sep 10 2024
R-4.3-win	OK	Sep 10 2024
R-4.3-mac	OK	Sep 10 2024

Exports:%>%as.enrichdat expoSheet genGSEA genInfo genORA getPubmed importCP importPanther importShinygo plot_theme plotEnrich plotEnrichAdv plotGSEA plotVenn plotVolcano simGO transId transProbe

Dependencies:AnnotationDbi ape aplot askpass BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 bitops blob cachem cli clusterProfiler codetools colorspace cowplot cpp11 crayon curl data.table DBI digest DOSE dplyr enrichplot europepmc fansi farver fastmap fastmatch fgsea formatR fs fst fstcore futile.logger futile.options generics geneset GenomeInfoDb GenomeInfoDbData ggforce ggfun ggnewscale ggplot2 ggplotify ggraph ggrepel ggtree ggvenn glue GO.db GOSemSim graphlayouts gridExtra gridGraphics gson gtable hms httr igraph IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lazyeval lifecycle magrittr MASS Matrix memoise mgcv mime munsell nlme openssl openxlsx patchwork pillar pkgconfig plogr plyr png polyclip prettyunits progress purrr qvalue R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl reshape2 rlang RSQLite S4Vectors scales scatterpie shadowtext snow stringi stringr sys systemfonts tibble tidygraph tidyr tidyselect tidytree treeio triebeard tweenr UCSC.utils urltools utf8 vctrs viridis viridisLite withr xml2 XVector yulab.utils zip zlibbioc

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Modify dataframe for enrichment plot	as.enrichdat
Datasets geneList entrez gene list with decreasing fold change value	biocOrg_name Datasets deg ensOrg_name geneList hsapiens_probe_platform keggOrg_name msig_category msig_org
Export list of data sets into different 'Excel' sheets	expoSheet
Gene Set Enrichment Analysis	genGSEA
Get gene related information	genInfo
Gene Over-Representation Enrichment Analysis	genORA
Get 'PubMed' paper records by searching abstract	getPubmed
Import 'clusterProfiler' result	importCP
Import 'Panther' web result	importPanther
Import 'shinyGO' web result	importShinygo
Themes for all plots	plot_theme
Plot for gene enrichment analysis of ORA method	plotEnrich
Advanced Plot for gene enrichment analysis of ORA method	plotEnrichAdv
Plot for gene enrichment analysis of GSEA method	plotGSEA
Venn plot for groups of genes	plotVenn
Volcano plot for differential expression analysis	plotVolcano
Simplify GO enrichment result	simGO
Transform id among symbol, entrezid, ensembl and uniprot.	transId
Transform probe id to symbol, entrezid, ensembl or uniprot.	transProbe