# Libraries
library(BSgenome.Umaydis.ENSMBL.UM1) # forged ustilago genome
library(ggplot2)
library(forcats)
library(tidyr)
library(dplyr)
library(tidyverse)
library(magrittr)
library(ggpp)
library(gginnards)
library(ggrepel)
library(ggpubr)
library(ggforce)
library(ggrastr)
library(viridis)
library(reshape2)
library(gprofiler2)load("C:/Users/Sri/Documents/Khd4/DGE_analysis_SM_PhD/Kathis_lab/hyperTRIBE/hyperTRIBE.rds")GO-term enrichment analysis with high confidence Khd4 targets were analysed using gprofiler2.
highConf.gene=data.frame(high.conf.khd4)
highConf.gene=unique(highConf.gene$gene.id)
HCgO= gost(query = highConf.gene,
organism = "umaydis", ordered_query = FALSE,
multi_query = FALSE, significant = TRUE, exclude_iea = FALSE,
measure_underrepresentation = FALSE, evcodes = TRUE,
user_threshold = 0.05, correction_method = "g_SCS",
domain_scope = "annotated", custom_bg = NULL,
numeric_ns = "", sources = NULL, as_short_link = FALSE)
#visualization
vis.HCgO<- gostplot(HCgO, capped = TRUE, interactive = TRUE)
vis.HCgO#get the link to download .gem files
gost(query = highConf.gene,
organism = "umaydis", ordered_query = FALSE,
multi_query = FALSE, significant = TRUE, exclude_iea = FALSE,
measure_underrepresentation = FALSE, evcodes = TRUE,
user_threshold = 0.05, correction_method = "g_SCS",
domain_scope = "annotated", custom_bg = NULL,
numeric_ns = "", sources = NULL, as_short_link = TRUE)[1] "https://biit.cs.ut.ee/gplink/l/rUSWagdKSW"sessionInfo()R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=English_Germany.utf8 LC_CTYPE=English_Germany.utf8
[3] LC_MONETARY=English_Germany.utf8 LC_NUMERIC=C
[5] LC_TIME=English_Germany.utf8
time zone: Europe/Berlin
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] gprofiler2_0.2.3 reshape2_1.4.4
[3] viridis_0.6.5 viridisLite_0.4.2
[5] ggrastr_1.0.2 ggforce_0.4.2
[7] ggpubr_0.6.0 ggrepel_0.9.5
[9] gginnards_0.2.0 ggpp_0.5.7
[11] magrittr_2.0.3 lubridate_1.9.3
[13] stringr_1.5.1 purrr_1.0.2
[15] readr_2.1.5 tibble_3.2.1
[17] tidyverse_2.0.0 dplyr_1.1.4
[19] tidyr_1.3.1 forcats_1.0.0
[21] ggplot2_3.5.1 BSgenome.Umaydis.ENSMBL.UM1_2.0.0
[23] BSgenome_1.70.2 rtracklayer_1.62.0
[25] BiocIO_1.12.0 Biostrings_2.70.1
[27] XVector_0.42.0 GenomicRanges_1.54.1
[29] GenomeInfoDb_1.38.8 IRanges_2.36.0
[31] S4Vectors_0.40.2 BiocGenerics_0.48.1
loaded via a namespace (and not attached):
[1] rstudioapi_0.16.0 jsonlite_1.8.8
[3] ggbeeswarm_0.7.2 GenomicFeatures_1.54.4
[5] farver_2.1.2 rmarkdown_2.27
[7] zlibbioc_1.48.0 vctrs_0.6.5
[9] memoise_2.0.1 Rsamtools_2.18.0
[11] RCurl_1.98-1.13 rstatix_0.7.2
[13] progress_1.2.3 htmltools_0.5.8.1
[15] S4Arrays_1.2.0 polynom_1.4-1
[17] curl_5.2.1 broom_1.0.6
[19] SparseArray_1.2.3 htmlwidgets_1.6.4
[21] plyr_1.8.9 cachem_1.0.8
[23] plotly_4.10.4 GenomicAlignments_1.38.0
[25] mime_0.12 lifecycle_1.0.4
[27] pkgconfig_2.0.3 Matrix_1.6-4
[29] R6_2.5.1 fastmap_1.1.1
[31] GenomeInfoDbData_1.2.11 MatrixGenerics_1.14.0
[33] shiny_1.8.1.1 digest_0.6.33
[35] colorspace_2.1-0 AnnotationDbi_1.64.1
[37] DESeq2_1.42.1 crosstalk_1.2.1
[39] RSQLite_2.3.7 filelock_1.0.3
[41] fansi_1.0.6 timechange_0.3.0
[43] httr_1.4.7 polyclip_1.10-6
[45] abind_1.4-5 compiler_4.3.1
[47] bit64_4.0.5 withr_3.0.0
[49] backports_1.5.0 BiocParallel_1.36.0
[51] carData_3.0-5 DBI_1.2.3
[53] biomaRt_2.58.2 ggsignif_0.6.4
[55] MASS_7.3-60 rappdirs_0.3.3
[57] DelayedArray_0.28.0 rjson_0.2.21
[59] tools_4.3.1 vipor_0.4.7
[61] beeswarm_0.4.0 httpuv_1.6.15
[63] glue_1.6.2 restfulr_0.0.15
[65] promises_1.3.0 grid_4.3.1
[67] ggvenn_0.1.10 generics_0.1.3
[69] gtable_0.3.5 tzdb_0.4.0
[71] data.table_1.15.4 hms_1.1.3
[73] xml2_1.3.6 car_3.1-2
[75] utf8_1.2.4 pillar_1.9.0
[77] later_1.3.2 tweenr_2.0.3
[79] BiocFileCache_2.10.2 lattice_0.22-5
[81] bit_4.0.5 tidyselect_1.2.1
[83] locfit_1.5-9.10 knitr_1.47
[85] gridExtra_2.3 SummarizedExperiment_1.32.0
[87] xfun_0.45 Biobase_2.62.0
[89] matrixStats_1.2.0 stringi_1.8.3
[91] lazyeval_0.2.2 yaml_2.3.7
[93] evaluate_0.24.0 codetools_0.2-20
[95] cli_3.6.1 xtable_1.8-4
[97] munsell_0.5.1 Rcpp_1.0.12
[99] dbplyr_2.5.0 png_0.1-8
[101] XML_3.99-0.16.1 parallel_4.3.1
[103] blob_1.2.4 prettyunits_1.2.0
[105] bitops_1.0-7 scales_1.3.0
[107] crayon_1.5.3 rlang_1.1.1
[109] KEGGREST_1.42.0 cowplot_1.1.3