Last updated: 2025-02-27

Checks: 7 0

Knit directory: locust-comparative-genomics/

This reproducible R Markdown analysis was created with workflowr (version 1.7.1). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

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

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: relative

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Repository version: f67d46e

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version f67d46e. 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:
    Ignored:    .DS_Store
    Ignored:    analysis/.DS_Store
    Ignored:    analysis/.Rhistory
    Ignored:    data/.DS_Store
    Ignored:    data/DEG_results/.DS_Store
    Ignored:    data/DEG_results/Bulk_RNAseq/.DS_Store
    Ignored:    data/DEG_results/Bulk_RNAseq/americana/.DS_Store
    Ignored:    data/DEG_results/Bulk_RNAseq/cancellata/.DS_Store
    Ignored:    data/DEG_results/Bulk_RNAseq/cubense/.DS_Store
    Ignored:    data/DEG_results/Bulk_RNAseq/davidO/.DS_Store
    Ignored:    data/DEG_results/Bulk_RNAseq/gregaria/.DS_Store
    Ignored:    data/DEG_results/Bulk_RNAseq/nitens/.DS_Store
    Ignored:    data/DEG_results/Bulk_RNAseq/piceifrons/.DS_Store
    Ignored:    data/DEG_results/RNAi/.DS_Store
    Ignored:    data/DEG_results/RNAi/All/.DS_Store
    Ignored:    data/DEG_results/RNAi/All_control/.DS_Store
    Ignored:    data/DEG_results/RNAi/All_no_rRNA/.DS_Store
    Ignored:    data/DEG_results/RNAi/Head/.DS_Store
    Ignored:    data/DEG_results/RNAi/Head_control/.DS_Store
    Ignored:    data/DEG_results/RNAi/Head_no_rRNA/.DS_Store
    Ignored:    data/DEG_results/RNAi/Thorax/.DS_Store
    Ignored:    data/DEG_results/RNAi/Thorax_no_rRNA/.DS_Store
    Ignored:    data/DEG_results/gregaria/
    Ignored:    data/DEG_results/single_cell/.DS_Store
    Ignored:    data/WGCNA/.DS_Store
    Ignored:    data/WGCNA/input/.DS_Store
    Ignored:    data/WGCNA/input/Bulk_RNAseq/.DS_Store
    Ignored:    data/WGCNA/output/
    Ignored:    data/behavioral_data/.DS_Store
    Ignored:    data/behavioral_data/Raw_data/.DS_Store
    Ignored:    data/custom_sgregaria_orgdb/.DS_Store
    Ignored:    data/list/.DS_Store
    Ignored:    data/list/Bulk_RNAseq/.DS_Store
    Ignored:    data/list/GO_Annotations/.DS_Store
    Ignored:    data/orthofinder/.DS_Store
    Ignored:    data/orthofinder/Polyneoptera/.DS_Store
    Ignored:    data/orthofinder/Polyneoptera/Results_I2/.DS_Store
    Ignored:    data/orthofinder/Polyneoptera/Results_I2/Orthogroups/.DS_Store
    Ignored:    data/orthofinder/Polyneoptera/Results_I5/.DS_Store
    Ignored:    data/orthofinder/Polyneoptera/Results_I5/Orthogroups/.DS_Store
    Ignored:    data/orthofinder/Schistocerca/.DS_Store
    Ignored:    data/orthofinder/Schistocerca/Results_I2/.DS_Store
    Ignored:    data/orthofinder/Schistocerca/Results_I2/Orthogroups/.DS_Store
    Ignored:    data/orthofinder/Schistocerca/Results_I5/.DS_Store
    Ignored:    data/orthofinder/Schistocerca/Results_I5/Orthogroups/.DS_Store
    Ignored:    data/overlap/.DS_Store
    Ignored:    data/overlap/Bulk_RNAseq/.DS_Store
    Ignored:    data/overlap/Bulk_RNAseq/cancellata/
    Ignored:    data/readcounts/.DS_Store
    Ignored:    data/readcounts/Bulk_RNAseq/.DS_Store
    Ignored:    data/readcounts/RNAi/.DS_Store

Untracked files:
    Untracked:  data/RefSeq/
    Untracked:  data/list/RNAi/Head_RNAi_noninjectedsample_list2.csv

Unstaged changes:
    Modified:   data/DEG_results/RNAi/Head/UNCH_vs_GFP/volcano_plot_UNCH_vs_GFP.tiff
    Modified:   data/DEG_results/RNAi/Head_no_rRNA/UNCH_vs_GFP/volcano_plot_UNCH_vs_GFP.tiff
    Modified:   data/readcounts/Bulk_RNAseq/03-gregaria-DESeq2/SGRE-HEAD-CRD-1_MERGE_counts.txt

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/1_team-science.Rmd) and HTML (docs/1_team-science.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
Rmd faf2db3 Maeva TECHER 2025-01-13 update markdown
html faf2db3 Maeva TECHER 2025-01-13 update markdown
html 3fa8e62 Maeva TECHER 2024-11-09 updated analysis
html edb70fe Maeva TECHER 2024-11-08 overlap and deg results created
html ba35b82 Maeva A. TECHER 2024-06-20 Build site.
html 4246194 Maeva A. TECHER 2024-01-30 Build site.
html f701a01 Maeva A. TECHER 2024-01-30 reupdate
html b8c43a8 Maeva A. TECHER 2024-01-24 Build site.
html 1b09cbe Maeva A. TECHER 2024-01-24 remove
html 2aa74b3 Maeva A. TECHER 2024-01-24 Build site.
Rmd f8c6b70 Maeva A. TECHER 2024-01-24 wflow_publish("analysis/1_team-science.Rmd")
html 9cf4d78 Maeva A. TECHER 2023-12-18 Build site.
Rmd 53877fa Maeva A. TECHER 2023-12-18 add pages

Flagship paper committee for the whole paper

Hojun, Greg, Erez/Olga and Anna (in no particular order)

Authors and Affiliations (arbitrary order)

All should have the BPRI as an affiliation.

USDA

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

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

Tyler J. Simmonds (two affiliations)

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

Oak Ridge Institute for Science and Education, P.O. Box 117, Oak Ridge, TN 37831, 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

Amanda R. Stahlke (two affiliations)

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

Anna K. Childers

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

Monica Poelchau

USDA-ARS, National Agricultural Library, 10301 Baltimore Ave, Beltsville, MD 20705

Texas A&M University

Hojun Song

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

Gregory A. Sword

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

Maeva A. Techer

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

Audelia Mechti

Ecology and Evolutionary Biology Interdisciplinary Doctoral Program, Texas A&M University, College Station, TX, 77843-2475, USA

Baylor College of Medicine

Olga Dudchenko

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

Erez Liberman Aiden

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

David Bellini

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

Stephen Richards

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

Fabrizio Gabbiani

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

Extended BPRI institutes

Bert Foquet

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

#Authors contribution

Name Conceptualization Sampling Data generation Data analysis Data curation Visualization Writing Supervision Admin & Funding
Author1 X X X X X X X 

sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.3

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_1.7.1

loaded via a namespace (and not attached):
 [1] vctrs_0.6.5       httr_1.4.7        cli_3.6.4         knitr_1.49       
 [5] rlang_1.1.5       xfun_0.51         stringi_1.8.4     processx_3.8.6   
 [9] promises_1.3.2    jsonlite_1.9.0    glue_1.8.0        rprojroot_2.0.4  
[13] git2r_0.35.0      htmltools_0.5.8.1 httpuv_1.6.15     ps_1.9.0         
[17] sass_0.4.9        rmarkdown_2.29    jquerylib_0.1.4   tibble_3.2.1     
[21] evaluate_1.0.3    fastmap_1.2.0     yaml_2.3.10       lifecycle_1.0.4  
[25] whisker_0.4.1     stringr_1.5.1     compiler_4.4.2    fs_1.6.5         
[29] pkgconfig_2.0.3   Rcpp_1.0.14       rstudioapi_0.17.1 later_1.4.1      
[33] digest_0.6.37     R6_2.6.1          pillar_1.10.1     callr_3.7.6      
[37] magrittr_2.0.3    bslib_0.9.0       tools_4.4.2       cachem_1.1.0     
[41] getPass_0.2-4