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Last updated: 2026-04-06

Checks: 7 0

Knit directory: locust-comparative-genomics/

This reproducible R Markdown analysis was created with workflowr (version 1.7.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

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R Markdown file: up-to-date

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Environment: empty

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Seed: set.seed(20221025)

The command set.seed(20221025) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

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Cache: none

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File paths: relative

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Repository version: 536b969

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The results in this page were generated with repository version 536b969. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:

Ignored files:
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    Modified:   data/cafe5_results/Base_change_FILE/piceifrons/Expansion/GO_MF_dotplot_piceifrons_Expansion_cafe.pdf
    Modified:   data/cafe5_results/Base_change_FILE/piceifrons/Expansion/KEGG_dotplot_piceifrons_Expansion_cafe.pdf
    Modified:   data/cafe5_results/Base_change_FILE/piceifrons/Expansion/KEGG_enrichment_piceifrons_Expansion_cafe.csv
    Modified:   data/cafe5_results/Base_change_FILE/piceifrons/Expansion/enrich_KEGG_piceifrons_Expansion_cafe.txt
    Modified:   data/cafe5_results/Gene_count_FILE/GO_BP_heatmap_top15.pdf
    Modified:   data/cafe5_results/Gene_count_FILE/GO_CC_heatmap_top15.pdf
    Modified:   data/cafe5_results/Gene_count_FILE/GO_MF_heatmap_top15.pdf
    Modified:   data/cafe5_results/Gene_count_FILE/KEGG_subcategory_faceted_heatmap_Count.pdf
    Modified:   data/cafe5_results/Gene_count_FILE/americana/GO_BP_dotplot_americana_cafe.pdf
    Modified:   data/cafe5_results/Gene_count_FILE/americana/GO_CC_dotplot_americana_cafe.pdf
    Modified:   data/cafe5_results/Gene_count_FILE/americana/GO_MF_dotplot_americana_cafe.pdf
    Modified:   data/cafe5_results/Gene_count_FILE/americana/KEGG_dotplot_americana_cafe.pdf
    Modified:   data/cafe5_results/Gene_count_FILE/americana/KEGG_enrichment_americana_cafe.csv
    Modified:   data/cafe5_results/Gene_count_FILE/americana/enrich_KEGG_americana_cafe.txt
    Modified:   data/cafe5_results/Gene_count_FILE/cancellata/GO_BP_dotplot_cancellata_cafe.pdf
    Modified:   data/cafe5_results/Gene_count_FILE/cancellata/GO_CC_dotplot_cancellata_cafe.pdf
    Modified:   data/cafe5_results/Gene_count_FILE/cancellata/GO_MF_dotplot_cancellata_cafe.pdf
    Modified:   data/cafe5_results/Gene_count_FILE/cancellata/KEGG_dotplot_cancellata_cafe.pdf
    Modified:   data/cafe5_results/Gene_count_FILE/cancellata/KEGG_enrichment_cancellata_cafe.csv
    Modified:   data/cafe5_results/Gene_count_FILE/cancellata/enrich_KEGG_cancellata_cafe.txt
    Modified:   data/cafe5_results/Gene_count_FILE/cubense/GO_BP_dotplot_cubense_cafe.pdf
    Modified:   data/cafe5_results/Gene_count_FILE/cubense/GO_CC_dotplot_cubense_cafe.pdf
    Modified:   data/cafe5_results/Gene_count_FILE/cubense/GO_MF_dotplot_cubense_cafe.pdf
    Modified:   data/cafe5_results/Gene_count_FILE/cubense/KEGG_dotplot_cubense_cafe.pdf
    Modified:   data/cafe5_results/Gene_count_FILE/cubense/KEGG_enrichment_cubense_cafe.csv
    Modified:   data/cafe5_results/Gene_count_FILE/cubense/enrich_KEGG_cubense_cafe.txt
    Modified:   data/cafe5_results/Gene_count_FILE/gregaria/GO_BP_dotplot_gregaria_cafe.pdf
    Modified:   data/cafe5_results/Gene_count_FILE/gregaria/GO_CC_dotplot_gregaria_cafe.pdf
    Modified:   data/cafe5_results/Gene_count_FILE/gregaria/GO_MF_dotplot_gregaria_cafe.pdf
    Modified:   data/cafe5_results/Gene_count_FILE/gregaria/KEGG_dotplot_gregaria_cafe.pdf
    Modified:   data/cafe5_results/Gene_count_FILE/gregaria/KEGG_enrichment_gregaria_cafe.csv
    Modified:   data/cafe5_results/Gene_count_FILE/gregaria/enrich_KEGG_gregaria_cafe.txt
    Modified:   data/cafe5_results/Gene_count_FILE/locusta/GO_BP_dotplot_locusta_cafe.pdf
    Modified:   data/cafe5_results/Gene_count_FILE/locusta/GO_CC_dotplot_locusta_cafe.pdf
    Modified:   data/cafe5_results/Gene_count_FILE/locusta/GO_MF_dotplot_locusta_cafe.pdf
    Modified:   data/cafe5_results/Gene_count_FILE/locusta/KEGG_dotplot_locusta_cafe.pdf
    Modified:   data/cafe5_results/Gene_count_FILE/locusta/KEGG_enrichment_locusta_cafe.csv
    Modified:   data/cafe5_results/Gene_count_FILE/locusta/enrich_KEGG_locusta_cafe.txt
    Modified:   data/cafe5_results/Gene_count_FILE/nitens/GO_BP_dotplot_nitens_cafe.pdf
    Modified:   data/cafe5_results/Gene_count_FILE/nitens/GO_CC_dotplot_nitens_cafe.pdf
    Modified:   data/cafe5_results/Gene_count_FILE/nitens/GO_MF_dotplot_nitens_cafe.pdf
    Modified:   data/cafe5_results/Gene_count_FILE/nitens/KEGG_dotplot_nitens_cafe.pdf
    Modified:   data/cafe5_results/Gene_count_FILE/nitens/KEGG_enrichment_nitens_cafe.csv
    Modified:   data/cafe5_results/Gene_count_FILE/nitens/enrich_KEGG_nitens_cafe.txt
    Modified:   data/cafe5_results/Gene_count_FILE/piceifrons/GO_BP_dotplot_piceifrons_cafe.pdf
    Modified:   data/cafe5_results/Gene_count_FILE/piceifrons/GO_CC_dotplot_piceifrons_cafe.pdf
    Modified:   data/cafe5_results/Gene_count_FILE/piceifrons/GO_MF_dotplot_piceifrons_cafe.pdf
    Modified:   data/cafe5_results/Gene_count_FILE/piceifrons/KEGG_dotplot_piceifrons_cafe.pdf
    Modified:   data/cafe5_results/Gene_count_FILE/piceifrons/KEGG_enrichment_piceifrons_cafe.csv
    Modified:   data/cafe5_results/Gene_count_FILE/piceifrons/enrich_KEGG_piceifrons_cafe.txt

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Authors and Affiliations (arbitrary order)

Maéva A. Techer

Department of Entomology, Texas A&M University, College Station, TX, 77843-2475, USA

School of Sustainability, Arizona State University, Tempe, AZ, USA

Sheina B. Sim

USDA, Agricultural Research Service, Daniel K Inouye U.S. Pacific Basin Agricultural Research Center, Tropical Pest Genetics and Molecular Biology Research Unit, 64 Nowelo Street, Hilo, HI 96720, USA

Olga Dudchenko

The Center for Genome Architecture, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States

Center for Theoretical Biological Physics and Department of Biosciences, Rice University, Houston, TX, United States

Anna K. Childers

USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Bee Research Laboratory, 10300 Baltimore Avenue, Beltsville, MD 20705, USA

Julianne Allred

Department of Entomology, Texas A&M University, College Station, TX, 77843-2475, USA

Emily Baker

Department of Entomology, Texas A&M University, College Station, TX, 77843-2475, USA

School of Life Sciences, Arizona State University, Tempe, AZ 85282

David Mario Bellini

Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA

Devon Boland

Texas A&M Institute of Genome Sciences & Society (TIGSS), College Station, TX, USA

Herman A. Dierick

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA

Richard B. Dewell

Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA

Bert Foquet

Mcguire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611-2710, USA

Scott M. Geib

USDA, Agricultural Research Service, Daniel K Inouye U.S. Pacific Basin Agricultural Research Center, Tropical Pest Genetics and Molecular Biology Research Unit, 64 Nowelo Street, Hilo, HI 96720, USA

Ruqayya Khan

The Center for Genome Architecture, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States

Center for Theoretical Biological Physics and Department of Biosciences, Rice University, Houston, TX, United States

Richelle Marquess

Department of Entomology, Texas A&M University, College Station, TX, 77843-2475, USA

Audélia M. C. Mechti

Department of Entomology, Texas A&M University, College Station, TX, 77843-2475, USA

Martina E. Pocco

Centro de Estudios Parasitológicos y de Vectores (CEPAVE), CONICET-UNLP, Boulevard 120 s/n e/Av.60 y calle 64, (1900) La Plata, Argentina

División Entomología, Museo de La Plata, Universidad Nacional de la Plata (UNLP), Argentina

Kathryn Puperi

Department of Entomology, Texas A&M University, College Station, TX, 77843-2475, USA

Seema Rana

Department of Entomology, Texas A&M University, College Station, TX, 77843-2475, USA

Stephen Richards

Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA

Brian Scheffler

USDA, Agricultural Research Service, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, 141 Experiment Station Road, Stoneville, MS 38776, USA

Tyler J. Simmonds

University of Georgia, College of Agricultural & Environmental Sciences, 136 Cedar St., Building C, Room 418, Athens, GA 30602

Amanda R. Stahlke

USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Bee Research Laboratory, 10300 Baltimore Avenue, Beltsville, MD 20705, USA

Department of Biological Sciences, Colorado Mesa University, Grand Junction, CO, 81051, USA

David Weisz

The Center for Genome Architecture, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States

Center for Theoretical Biological Physics and Department of Biosciences, Rice University, Houston, TX, United States

Fabrizio Gabbiani

Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA

Gregory A. Sword

Department of Entomology, Texas A&M University, College Station, TX, 77843-2475, USA

Erez Lieberman Aiden

The Center for Genome Architecture, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States

Center for Theoretical Biological Physics and Department of Biosciences, Rice University, Houston, TX, United States

Hojun Song

Department of Entomology, Texas A&M University, College Station, TX, 77843-2475, USA

School of Life Sciences, Arizona State University, Tempe, AZ 85282

Session information

sessionInfo()

R version 4.4.2 (2024-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.7.4

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Asia/Tokyo
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] workflowr_1.7.2

loaded via a namespace (and not attached):
 [1] vctrs_0.7.0       httr_1.4.7        cli_3.6.5         knitr_1.51       
 [5] rlang_1.1.7       xfun_0.56         stringi_1.8.7     otel_0.2.0       
 [9] processx_3.8.6    promises_1.5.0    jsonlite_2.0.0    glue_1.8.0       
[13] rprojroot_2.1.1   git2r_0.36.2      htmltools_0.5.9   httpuv_1.6.16    
[17] ps_1.9.1          sass_0.4.10       rmarkdown_2.30    tibble_3.3.1     
[21] jquerylib_0.1.4   evaluate_1.0.5    fastmap_1.2.0     yaml_2.3.12      
[25] lifecycle_1.0.5   whisker_0.4.1     stringr_1.6.0     compiler_4.4.2   
[29] fs_1.6.6          pkgconfig_2.0.3   Rcpp_1.1.1        rstudioapi_0.18.0
[33] later_1.4.5       digest_0.6.39     R6_2.6.1          pillar_1.11.1    
[37] callr_3.7.6       magrittr_2.0.4    bslib_0.9.0       tools_4.4.2      
[41] cachem_1.1.0      getPass_0.2-4