Show the code

    # 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)

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    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.

Show the code

    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

Show the code

    #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"

Show the code

    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

##### Source Code

    ---
    title: "GO-term analysis"
    date: last-modified
    author:
       - name:  "Srimeenakshi Sankaranarayanan"
    title-block-banner: true
    format:
        html:
            theme: flatly
            self-contained: true
            code-fold: true
            code-tools: true
            code-summary: "Show the code"
            toc: true
            number-sections: true
            anchor-sections: true
    editor: visual
    execute:
      echo: true
      error: false
      warning: false
      message: false
    ---

    ```{r}
    # 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)
    ```

    ```{r}
    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.

    ```{r}
    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
    ```

    ```{r}
    #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)
    ```

    ```{r}
    sessionInfo()
    ```