Last updated: 2025-02-11
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Knit directory:
locust-comparative-genomics/
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Deleted: data/DEG-results/DESeq2_sigresults_Thorax_togregaria_americana.csv
Deleted: data/DEG-results/DESeq2_sigresults_Thorax_togregaria_cancellata.csv
Deleted: data/DEG-results/DESeq2_sigresults_Thorax_togregaria_cubense.csv
Deleted: data/DEG-results/DESeq2_sigresults_Thorax_togregaria_gregaria.csv
Deleted: data/DEG-results/DESeq2_sigresults_Thorax_togregaria_nitens.csv
Deleted: data/DEG-results/DESeq2_sigresults_Thorax_togregaria_piceifrons.csv
Deleted: data/DEG-results/DESeq2_sigresults_head_americana.csv
Deleted: data/DEG-results/DESeq2_sigresults_head_cancellata.csv
Deleted: data/DEG-results/DESeq2_sigresults_head_cubense.csv
Deleted: data/DEG-results/DESeq2_sigresults_head_gregaria.csv
Deleted: data/DEG-results/DESeq2_sigresults_head_nitens.csv
Deleted: data/DEG-results/DESeq2_sigresults_head_piceifrons.csv
Deleted: data/DEG-results/GO10_enrichment_Head_americana_custom.csv
Deleted: data/DEG-results/GO10_enrichment_Head_cancellata_custom.csv
Deleted: data/DEG-results/GO10_enrichment_Head_cubense_custom.csv
Deleted: data/DEG-results/GO10_enrichment_Head_gregaria_custom.csv
Deleted: data/DEG-results/GO10_enrichment_Head_nitens_custom.csv
Deleted: data/DEG-results/GO10_enrichment_Head_piceifrons_custom.csv
Deleted: data/DEG-results/GO10_enrichment_Thorax_americana_custom.csv
Deleted: data/DEG-results/GO10_enrichment_Thorax_cancellata_custom.csv
Deleted: data/DEG-results/GO10_enrichment_Thorax_cubense_custom.csv
Deleted: data/DEG-results/GO10_enrichment_Thorax_gregaria_custom.csv
Deleted: data/DEG-results/GO10_enrichment_Thorax_nitens_custom.csv
Deleted: data/DEG-results/GO10_enrichment_Thorax_piceifrons_custom.csv
Deleted: data/DEG-results/GO30_enrichment_Head_americana_custom.csv
Deleted: data/DEG-results/GO30_enrichment_Head_cancellata_custom.csv
Deleted: data/DEG-results/GO30_enrichment_Head_cubense_custom.csv
Deleted: data/DEG-results/GO30_enrichment_Head_gregaria_custom.csv
Deleted: data/DEG-results/GO30_enrichment_Head_nitens_custom.csv
Deleted: data/DEG-results/GO30_enrichment_Head_piceifrons_custom.csv
Deleted: data/DEG-results/GO30_enrichment_Thorax_americana_custom.csv
Deleted: data/DEG-results/GO30_enrichment_Thorax_cancellata_custom.csv
Deleted: data/DEG-results/GO30_enrichment_Thorax_cubense_custom.csv
Deleted: data/DEG-results/GO30_enrichment_Thorax_gregaria_custom.csv
Deleted: data/DEG-results/GO30_enrichment_Thorax_nitens_custom.csv
Deleted: data/DEG-results/GO30_enrichment_Thorax_piceifrons_custom.csv
Deleted: data/DEG-results/GO_enrichment_head_americana_custom.csv
Deleted: data/DEG-results/GO_enrichment_head_cancellata_custom.csv
Deleted: data/DEG-results/GO_enrichment_head_cubense_custom.csv
Deleted: data/DEG-results/GO_enrichment_head_gregaria_custom.csv
Deleted: data/DEG-results/GO_enrichment_head_gregaria_custom_top10.csv
Deleted: data/DEG-results/GO_enrichment_head_nitens_custom.csv
Deleted: data/DEG-results/GO_enrichment_head_piceifrons_custom.csv
Deleted: data/DEG-results/overlapping_genes_head_thorax_americana.csv
Deleted: data/DEG-results/overlapping_genes_head_thorax_cancellata.csv
Deleted: data/DEG-results/overlapping_genes_head_thorax_cubense.csv
Deleted: data/DEG-results/overlapping_genes_head_thorax_gregaria.csv
Deleted: data/DEG-results/overlapping_genes_head_thorax_nitens.csv
Deleted: data/DEG-results/overlapping_genes_head_thorax_piceifrons.csv
Deleted: data/DEG-results/scatter_plot_overlapping_genes_americana.png
Deleted: data/DEG-results/scatter_plot_overlapping_genes_cancellata.png
Deleted: data/DEG-results/scatter_plot_overlapping_genes_cubense.png
Deleted: data/DEG-results/scatter_plot_overlapping_genes_gregaria.png
Deleted: data/DEG-results/scatter_plot_overlapping_genes_nitens.png
Deleted: data/DEG-results/scatter_plot_overlapping_genes_piceifrons.png
Deleted: data/list/Head_americana_WGCNA.txt
Deleted: data/list/Head_americana_nooutliers.txt
Deleted: data/list/Head_cancellata_WGCNA.txt
Deleted: data/list/Head_cancellata_nooutliers.txt
Deleted: data/list/Head_cubense_WGCNA.txt
Deleted: data/list/Head_cubense_nooutliers.txt
Deleted: data/list/Head_gregaria.txt
Deleted: data/list/Head_gregaria_WGCNA.txt
Deleted: data/list/Head_nitens_WGCNA.txt
Deleted: data/list/Head_nitens_nooutliers.txt
Deleted: data/list/Head_piceifrons_WGCNA.txt
Deleted: data/list/Head_piceifrons_nooutliers.txt
Deleted: data/list/Thorax_americana_WGCNA.txt
Deleted: data/list/Thorax_americana_nooutliers.txt
Deleted: data/list/Thorax_cancellata_WGCNA.txt
Deleted: data/list/Thorax_cancellata_nooutliers.txt
Deleted: data/list/Thorax_cubense_WGCNA.txt
Deleted: data/list/Thorax_cubense_nooutliers.txt
Deleted: data/list/Thorax_gregaria_WGCNA.txt
Deleted: data/list/Thorax_gregaria_nooutliers.txt
Deleted: data/list/Thorax_nitens_WGCNA.txt
Deleted: data/list/Thorax_nitens_nooutliers.txt
Deleted: data/list/Thorax_piceifrons.txt
Deleted: data/list/Thorax_piceifrons_WGCNA.txt
Modified: data/orthofinder/Polyneoptera/Results_I2/Orthogroups_13species_Jan2025.txt
Modified: data/orthofinder/Polyneoptera/Results_I2/Orthogroups_genesprotein_Schisto_Jan2025.txt
Modified: data/orthofinder/Polyneoptera/Results_I2/Orthogroups_genesproteinbiotype_13species_Jan2025.csv
Modified: data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_A. simplex.pdf
Modified: data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_B. rossius.pdf
Modified: data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_C. secundus.pdf
Modified: data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_D. australis.pdf
Modified: data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_G. bimaculatus.pdf
Modified: data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_G. longicornis.pdf
Modified: data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_P. americana.pdf
Modified: data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_americana.pdf
Modified: data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_cancellata.pdf
Modified: data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_cubense.pdf
Modified: data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_gregaria.pdf
Modified: data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_nitens.pdf
Modified: data/orthofinder/Polyneoptera/Results_I2/Plots_Polyneoptera/VerticalStackedBar_piceifrons.pdf
Modified: data/orthofinder/Polyneoptera/Results_I2/SingleCopyOrthogroups_genesprotein_13species_Jan2025.txt
Modified: data/orthofinder/Schistocerca/Results_I2/Orthogroups_Schistocerca_Jan2025.txt
Modified: data/orthofinder/Schistocerca/Results_I2/Orthogroups_genesproteinbiotype_Schistocerca_Jan2025.csv
Modified: data/orthofinder/Schistocerca/Results_I2/Plots_Schistocerca/VerticalStackedBar_americana.pdf
Modified: data/orthofinder/Schistocerca/Results_I2/Plots_Schistocerca/VerticalStackedBar_cancellata.pdf
Modified: data/orthofinder/Schistocerca/Results_I2/Plots_Schistocerca/VerticalStackedBar_cubense.pdf
Modified: data/orthofinder/Schistocerca/Results_I2/Plots_Schistocerca/VerticalStackedBar_gregaria.pdf
Modified: data/orthofinder/Schistocerca/Results_I2/Plots_Schistocerca/VerticalStackedBar_nitens.pdf
Modified: data/orthofinder/Schistocerca/Results_I2/Plots_Schistocerca/VerticalStackedBar_piceifrons.pdf
Modified: data/orthofinder/Schistocerca/Results_I2/SingleCopyOrthogroups_genesprotein_6species_Jan2025.txt
Deleted: data/overlap/summary_DEGs_Orthogroups_togregaria.csv
Deleted: data/readcounts/03-americana-DESeq2-togregaria/SAMER_G_Crd_SRR11815241_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2-togregaria/SAMER_G_Crd_SRR11815242_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2-togregaria/SAMER_G_Crd_SRR11815243_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2-togregaria/SAMER_G_Crd_SRR11815244_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2-togregaria/SAMER_G_Crd_SRR11815245_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2-togregaria/SAMER_G_Crd_SRR11815246_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2-togregaria/SAMER_G_Crd_SRR11815247_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2-togregaria/SAMER_G_Crd_SRR11815248_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2-togregaria/SAMER_G_Crd_SRR11815249_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2-togregaria/SAMER_G_Crd_SRR11815250_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2-togregaria/SAMER_S_Iso_SRR11815252_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2-togregaria/SAMER_S_Iso_SRR11815253_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2-togregaria/SAMER_S_Iso_SRR11815254_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2-togregaria/SAMER_S_Iso_SRR11815255_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2-togregaria/SAMER_S_Iso_SRR11815256_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2-togregaria/SAMER_S_Iso_SRR11815257_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2-togregaria/SAMER_S_Iso_SRR11815258_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2-togregaria/SAMER_S_Iso_SRR11815259_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2-togregaria/SAMER_S_Iso_SRR11815260_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2-togregaria/SAMER_S_Iso_SRR11815263_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_G_Crd_SRR11815241_counts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_G_Crd_SRR11815241_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_G_Crd_SRR11815242_counts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_G_Crd_SRR11815242_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_G_Crd_SRR11815243_counts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_G_Crd_SRR11815243_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_G_Crd_SRR11815244_counts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_G_Crd_SRR11815244_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_G_Crd_SRR11815245_counts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_G_Crd_SRR11815245_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_G_Crd_SRR11815246_counts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_G_Crd_SRR11815246_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_G_Crd_SRR11815247_counts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_G_Crd_SRR11815247_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_G_Crd_SRR11815248_counts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_G_Crd_SRR11815248_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_G_Crd_SRR11815249_counts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_G_Crd_SRR11815249_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_G_Crd_SRR11815250_counts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_G_Crd_SRR11815250_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_S_Iso_SRR11815252_counts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_S_Iso_SRR11815252_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_S_Iso_SRR11815253_counts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_S_Iso_SRR11815253_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_S_Iso_SRR11815254_counts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_S_Iso_SRR11815254_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_S_Iso_SRR11815255_counts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_S_Iso_SRR11815255_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_S_Iso_SRR11815256_counts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_S_Iso_SRR11815256_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_S_Iso_SRR11815257_counts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_S_Iso_SRR11815257_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_S_Iso_SRR11815258_counts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_S_Iso_SRR11815258_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_S_Iso_SRR11815259_counts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_S_Iso_SRR11815259_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_S_Iso_SRR11815260_counts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_S_Iso_SRR11815260_featurecounts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_S_Iso_SRR11815263_counts.txt
Deleted: data/readcounts/03-americana-DESeq2/SAMER_S_Iso_SRR11815263_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2-togregaria/SCANC_G_Crd_SRR17648042_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2-togregaria/SCANC_G_Crd_SRR17648043_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2-togregaria/SCANC_G_Crd_SRR17648048_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2-togregaria/SCANC_G_Crd_SRR17648049_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2-togregaria/SCANC_G_Crd_SRR17648056_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2-togregaria/SCANC_G_Crd_SRR17648057_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2-togregaria/SCANC_G_Crd_SRR17648058_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2-togregaria/SCANC_G_Crd_SRR17648059_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2-togregaria/SCANC_G_Crd_SRR17648060_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2-togregaria/SCANC_G_Crd_SRR17648061_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2-togregaria/SCANC_S_Iso_SRR17648044_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2-togregaria/SCANC_S_Iso_SRR17648045_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2-togregaria/SCANC_S_Iso_SRR17648046_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2-togregaria/SCANC_S_Iso_SRR17648047_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2-togregaria/SCANC_S_Iso_SRR17648050_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2-togregaria/SCANC_S_Iso_SRR17648051_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2-togregaria/SCANC_S_Iso_SRR17648052_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2-togregaria/SCANC_S_Iso_SRR17648053_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2-togregaria/SCANC_S_Iso_SRR17648054_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2-togregaria/SCANC_S_Iso_SRR17648055_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_G_Crd_SRR17648042_counts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_G_Crd_SRR17648042_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_G_Crd_SRR17648043_counts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_G_Crd_SRR17648043_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_G_Crd_SRR17648048_counts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_G_Crd_SRR17648048_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_G_Crd_SRR17648049_counts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_G_Crd_SRR17648049_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_G_Crd_SRR17648056_counts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_G_Crd_SRR17648056_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_G_Crd_SRR17648057_counts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_G_Crd_SRR17648057_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_G_Crd_SRR17648058_counts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_G_Crd_SRR17648058_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_G_Crd_SRR17648059_counts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_G_Crd_SRR17648059_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_G_Crd_SRR17648060_counts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_G_Crd_SRR17648060_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_G_Crd_SRR17648061_counts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_G_Crd_SRR17648061_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_S_Iso_SRR17648044_counts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_S_Iso_SRR17648044_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_S_Iso_SRR17648045_counts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_S_Iso_SRR17648045_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_S_Iso_SRR17648046_counts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_S_Iso_SRR17648046_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_S_Iso_SRR17648047_counts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_S_Iso_SRR17648047_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_S_Iso_SRR17648050_counts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_S_Iso_SRR17648050_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_S_Iso_SRR17648051_counts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_S_Iso_SRR17648051_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_S_Iso_SRR17648052_counts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_S_Iso_SRR17648052_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_S_Iso_SRR17648053_counts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_S_Iso_SRR17648053_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_S_Iso_SRR17648054_counts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_S_Iso_SRR17648054_featurecounts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_S_Iso_SRR17648055_counts.txt
Deleted: data/readcounts/03-cancellata-DESeq2/SCANC_S_Iso_SRR17648055_featurecounts.txt
Deleted: data/readcounts/03-cubense-DESeq2-togregaria/SSCUB_G_Crd_SRR11815219_featurecounts.txt
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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.
There are no past versions. Publish this analysis with
wflow_publish() to start tracking its development.
# Load necessary libraries
library(dplyr) # Data manipulation
library(tidyr) # Data transformation (pivot_wider)
library(readr) # Efficient CSV reading/writing
library(stringr) # String manipulation
library(purrr) # Functional programming (handling missing files)
library(tibble) # Improved dataframe handling
library(forcats) # Factor manipulation (optional, if needed for ordering)
library(tidyverse)
library(kableExtra)
library(DT)
# Path for all species
workDir <- "/Users/maevatecher/Documents/GitHub/locust-comparative-genomics/data"
allspecies_path <- file.path(workDir, "/list/13polyneoptera_geneid_ncbi.csv")
allspecies_df <- read.table(allspecies_path, sep = ",", header = TRUE, quote = "", fill = TRUE, stringsAsFactors = FALSE)
species_list <- c("gregaria", "piceifrons", "cancellata", "americana", "cubense", "nitens")
species_order <- c( "nitens", "cubense", "americana", "piceifrons", "cancellata", "gregaria")This table summarize the DEGs as well as the orthogroups it belongs using the DEGs mapped to gregaria.
# Load Orthogroup information
ortho_dir <- "/Users/maevatecher/Documents/GitHub/locust-comparative-genomics/data/orthofinder/Schistocerca"
input_file <- file.path(ortho_dir, "Results_I2/Orthogroups_genesproteinbiotype_Schistocerca_Jan2025.csv")
ortholog_df <- read_csv(input_file, trim_ws = TRUE)
# Replace NA values in the Orthogroup column with "Unassigned"
ortholog_df$Orthogroup[is.na(ortholog_df$Orthogroup)] <- "Unassigned"
# Ensure correct column names
if ("gene_id" %in% colnames(ortholog_df)) {
colnames(ortholog_df)[colnames(ortholog_df) == "gene_id"] <- "GeneID"
}
# Keep only relevant columns and ensure uniqueness
ortholog_df <- ortholog_df %>%
select(GeneID, GeneType, Orthogroup, Description, Species) %>%
distinct(GeneID, .keep_all = TRUE)
# Define species list
species_list <- c("gregaria", "piceifrons", "cancellata", "americana", "cubense", "nitens")
# Initialize an empty data frame for summary
summary_table <- data.frame()
# Loop through each species
for (species in species_list) {
message(paste("Processing:", species))
# Load DESeq2 results for Head and Thorax
head_file <- file.path(workDir, "DEG_results/Bulk_RNAseq", paste0("DESeq2_sigresults_Head_togregaria_", species, ".csv"))
thorax_file <- file.path(workDir, "DEG_results/Bulk_RNAseq", paste0("DESeq2_sigresults_Thorax_togregaria_", species, ".csv"))
# Check if files exist
if (!file.exists(head_file) || !file.exists(thorax_file)) {
message(paste("Missing DESeq2 results for:", species))
next
}
head_data <- read.csv(head_file, stringsAsFactors = FALSE)
thorax_data <- read.csv(thorax_file, stringsAsFactors = FALSE)
# Ensure GeneID column exists
if (!"GeneID" %in% colnames(head_data) && "X" %in% colnames(head_data)) {
colnames(head_data)[colnames(head_data) == "X"] <- "GeneID"
}
if (!"GeneID" %in% colnames(thorax_data) && "X" %in% colnames(thorax_data)) {
colnames(thorax_data)[colnames(thorax_data) == "X"] <- "GeneID"
}
# Convert GeneID to character
head_data$GeneID <- as.character(head_data$GeneID)
thorax_data$GeneID <- as.character(thorax_data$GeneID)
ortholog_df$GeneID <- as.character(ortholog_df$GeneID)
# Merge with Orthogroups and ensure Orthogroup is always character
head_merged <- left_join(head_data, ortholog_df, by = "GeneID") %>%
mutate(Orthogroup = as.character(ifelse(is.na(Orthogroup), "Unassigned", Orthogroup)))
thorax_merged <- left_join(thorax_data, ortholog_df, by = "GeneID") %>%
mutate(Orthogroup = as.character(ifelse(is.na(Orthogroup), "Unassigned", Orthogroup)))
# Classify DEGs and add Tissue + Species columns
head_merged <- head_merged %>%
mutate(
Status = case_when(
padj < 0.05 & log2FoldChange > 1 ~ "Upregulated",
padj < 0.05 & log2FoldChange < -1 ~ "Downregulated",
TRUE ~ "Not Significant"
),
Tissue = "Head", # Add Tissue column
Species = species # Add Species column (Fix!)
) %>%
select(GeneID, GeneType, Description, Orthogroup, Tissue, Species, Status) # Ensure Species column is included
thorax_merged <- thorax_merged %>%
mutate(
Status = case_when(
padj < 0.05 & log2FoldChange > 1 ~ "Upregulated",
padj < 0.05 & log2FoldChange < -1 ~ "Downregulated",
TRUE ~ "Not Significant"
),
Tissue = "Thorax", # Add Tissue column
Species = species # Add Species column (Fix!)
) %>%
select(GeneID, GeneType, Description, Orthogroup, Tissue, Species, Status) # Ensure Species column is included
# Combine results
summary_table <- bind_rows(summary_table, head_merged, thorax_merged)
}
# Pivot table to show Up/Down/Not Significant per species
summary_table_pivot <- summary_table %>%
pivot_wider(names_from = c(Species, Tissue), values_from = Status, values_fill = "Not Detected")
# Create a searchable DataTable with color formatting
datatable(
summary_table_pivot,
options = list(
pageLength = 50, # Show only the first 50 rows by default
scrollX = TRUE, # Enable horizontal scrolling if needed
autoWidth = TRUE, # Adjust column width automatically
searchHighlight = TRUE # Highlight search results
),
rownames = FALSE,
class = "compact" # Applies a smaller font size
) %>%
formatStyle(
columns = names(summary_table_pivot)[-c(1,2)], # Exclude Orthogroup and GeneID from color formatting
backgroundColor = styleEqual(
c("Upregulated", "Downregulated"),
c("lightcoral", "lightblue") # Red for Upregulated, Blue for Downregulated
),
color = styleEqual(
c("Upregulated", "Downregulated"),
c("white", "black") # White text for Upregulated, Black text for Downregulated
)
)# Save as CSV
output_file <- file.path(workDir, "overlap/summarySchistocerca_DEGs_Orthogroups_togregaria_Feb2025.csv")
write.csv(summary_table_pivot, output_file, row.names = FALSE)
message(paste("Summary table saved at:", output_file))This table summarize the DEGs as well as the orthogroups it belongs. Here
# Load Orthogroup information
ortho_dir <- "/Users/maevatecher/Documents/GitHub/locust-comparative-genomics/data/orthofinder/Schistocerca"
input_file <- file.path(ortho_dir, "Results_I2/Orthogroups_genesproteinbiotype_Schistocerca_Jan2025.csv")
ortholog_df <- read_csv(input_file, trim_ws = TRUE)
# Replace NA values in the Orthogroup column with "Unassigned"
ortholog_df$Orthogroup[is.na(ortholog_df$Orthogroup)] <- "Unassigned"
# Ensure correct column names
if ("gene_id" %in% colnames(ortholog_df)) {
colnames(ortholog_df)[colnames(ortholog_df) == "gene_id"] <- "GeneID"
}
# Keep only relevant columns and ensure uniqueness
ortholog_df <- ortholog_df %>%
select(GeneID, GeneType, Orthogroup, Description, Species) %>%
distinct(GeneID, .keep_all = TRUE)
# Define species list
species_list <- c("gregaria", "piceifrons", "cancellata", "americana", "cubense", "nitens")
# Initialize an empty data frame for summary
summary_table <- data.frame()
# Loop through each species
for (species in species_list) {
message(paste("Processing:", species))
# Load DESeq2 results for Head and Thorax
head_file <- file.path(workDir, "DEG_results/Bulk_RNAseq", paste0("DESeq2_sigresults_Head_", species, ".csv"))
thorax_file <- file.path(workDir, "DEG_results/Bulk_RNAseq", paste0("DESeq2_sigresults_Thorax_", species, ".csv"))
# Check if files exist
if (!file.exists(head_file) || !file.exists(thorax_file)) {
message(paste("Missing DESeq2 results for:", species))
next
}
head_data <- read.csv(head_file, stringsAsFactors = FALSE)
thorax_data <- read.csv(thorax_file, stringsAsFactors = FALSE)
# Ensure GeneID column exists
if (!"GeneID" %in% colnames(head_data) && "X" %in% colnames(head_data)) {
colnames(head_data)[colnames(head_data) == "X"] <- "GeneID"
}
if (!"GeneID" %in% colnames(thorax_data) && "X" %in% colnames(thorax_data)) {
colnames(thorax_data)[colnames(thorax_data) == "X"] <- "GeneID"
}
# Convert GeneID to character
head_data$GeneID <- as.character(head_data$GeneID)
thorax_data$GeneID <- as.character(thorax_data$GeneID)
ortholog_df$GeneID <- as.character(ortholog_df$GeneID)
# Merge with Orthogroups and ensure Orthogroup is always character
head_merged <- left_join(head_data, ortholog_df, by = "GeneID") %>%
mutate(Orthogroup = as.character(ifelse(is.na(Orthogroup), "Unassigned", Orthogroup)))
thorax_merged <- left_join(thorax_data, ortholog_df, by = "GeneID") %>%
mutate(Orthogroup = as.character(ifelse(is.na(Orthogroup), "Unassigned", Orthogroup)))
# Classify DEGs and add Tissue + Species columns
head_merged <- head_merged %>%
mutate(
Status = case_when(
padj < 0.05 & log2FoldChange > 1 ~ "Upregulated",
padj < 0.05 & log2FoldChange < -1 ~ "Downregulated",
TRUE ~ "Not Significant"
),
Tissue = "Head", # Add Tissue column
Species = species # Add Species column (Fix!)
) %>%
select(GeneID, GeneType, Description, Orthogroup, Tissue, Species, Status) # Ensure Species column is included
thorax_merged <- thorax_merged %>%
mutate(
Status = case_when(
padj < 0.05 & log2FoldChange > 1 ~ "Upregulated",
padj < 0.05 & log2FoldChange < -1 ~ "Downregulated",
TRUE ~ "Not Significant"
),
Tissue = "Thorax", # Add Tissue column
Species = species # Add Species column (Fix!)
) %>%
select(GeneID, GeneType, Description, Orthogroup, Tissue, Species, Status) # Ensure Species column is included
# Combine results
summary_table <- bind_rows(summary_table, head_merged, thorax_merged)
}
# Pivot table to show Up/Down/Not Significant per species
summary_table_pivot <- summary_table %>%
pivot_wider(names_from = c(Species, Tissue), values_from = Status, values_fill = "Not Detected")
# Create a searchable DataTable with color formatting
datatable(
summary_table_pivot,
options = list(
pageLength = 50, # Show only the first 50 rows by default
scrollX = TRUE, # Enable horizontal scrolling if needed
autoWidth = TRUE, # Adjust column width automatically
searchHighlight = TRUE # Highlight search results
),
rownames = FALSE,
class = "compact" # Applies a smaller font size
) %>%
formatStyle(
columns = names(summary_table_pivot)[-c(1,2)], # Exclude Orthogroup and GeneID from color formatting
backgroundColor = styleEqual(
c("Upregulated", "Downregulated"),
c("lightcoral", "lightblue") # Red for Upregulated, Blue for Downregulated
),
color = styleEqual(
c("Upregulated", "Downregulated"),
c("white", "black") # White text for Upregulated, Black text for Downregulated
)
)# Save as CSV
output_file <- file.path(workDir, "overlap/summarySchistocerca_DEGs_Orthogroups_Feb2025.csv")
write.csv(summary_table_pivot, output_file, row.names = FALSE)
message(paste("Summary table saved at:", output_file))This table summarize the DEGs as well as the orthogroups it belongs using the DEGs mapped to gregaria.
library(tidyverse)
# Load Orthogroup information
ortho_dir <- "/Users/maevatecher/Documents/GitHub/locust-comparative-genomics/data/orthofinder/Polyneoptera"
input_file <- file.path(ortho_dir, "Results_I2/Orthogroups_genesproteinbiotype_13species_Jan2025.csv")
ortholog_df <- read_csv(input_file, trim_ws = TRUE)
# Replace NA values in the Orthogroup column with "Unassigned"
ortholog_df$Orthogroup[is.na(ortholog_df$Orthogroup)] <- "Unassigned"
# Ensure correct column names
if ("gene_id" %in% colnames(ortholog_df)) {
colnames(ortholog_df)[colnames(ortholog_df) == "gene_id"] <- "GeneID"
}
# Keep only relevant columns and ensure uniqueness
ortholog_df <- ortholog_df %>%
select(GeneID, GeneType, Orthogroup, Description, Species) %>%
distinct(GeneID, .keep_all = TRUE)
# Define species list
species_list <- c("gregaria", "piceifrons", "cancellata", "americana", "cubense", "nitens")
# Initialize an empty data frame for summary
summary_table <- data.frame()
# Loop through each species
for (species in species_list) {
message(paste("Processing:", species))
# Load DESeq2 results for Head and Thorax
head_file <- file.path(workDir, "DEG_results/Bulk_RNAseq", paste0("DESeq2_sigresults_Head_togregaria_", species, ".csv"))
thorax_file <- file.path(workDir, "DEG_results/Bulk_RNAseq", paste0("DESeq2_sigresults_Thorax_togregaria_", species, ".csv"))
# Check if files exist
if (!file.exists(head_file) || !file.exists(thorax_file)) {
message(paste("Missing DESeq2 results for:", species))
next
}
head_data <- read.csv(head_file, stringsAsFactors = FALSE)
thorax_data <- read.csv(thorax_file, stringsAsFactors = FALSE)
# Ensure GeneID column exists
if (!"GeneID" %in% colnames(head_data) && "X" %in% colnames(head_data)) {
colnames(head_data)[colnames(head_data) == "X"] <- "GeneID"
}
if (!"GeneID" %in% colnames(thorax_data) && "X" %in% colnames(thorax_data)) {
colnames(thorax_data)[colnames(thorax_data) == "X"] <- "GeneID"
}
# Convert GeneID to character
head_data$GeneID <- as.character(head_data$GeneID)
thorax_data$GeneID <- as.character(thorax_data$GeneID)
ortholog_df$GeneID <- as.character(ortholog_df$GeneID)
# Merge with Orthogroups and ensure Orthogroup is always character
head_merged <- left_join(head_data, ortholog_df, by = "GeneID") %>%
mutate(Orthogroup = as.character(ifelse(is.na(Orthogroup), "Unassigned", Orthogroup)))
thorax_merged <- left_join(thorax_data, ortholog_df, by = "GeneID") %>%
mutate(Orthogroup = as.character(ifelse(is.na(Orthogroup), "Unassigned", Orthogroup)))
# Classify DEGs and add Tissue + Species columns
head_merged <- head_merged %>%
mutate(
Status = case_when(
padj < 0.05 & log2FoldChange > 1 ~ "Upregulated",
padj < 0.05 & log2FoldChange < -1 ~ "Downregulated",
TRUE ~ "Not Significant"
),
Tissue = "Head", # Add Tissue column
Species = species # Add Species column (Fix!)
) %>%
select(GeneID, GeneType, Description, Orthogroup, Tissue, Species, Status) # Ensure Species column is included
thorax_merged <- thorax_merged %>%
mutate(
Status = case_when(
padj < 0.05 & log2FoldChange > 1 ~ "Upregulated",
padj < 0.05 & log2FoldChange < -1 ~ "Downregulated",
TRUE ~ "Not Significant"
),
Tissue = "Thorax", # Add Tissue column
Species = species # Add Species column (Fix!)
) %>%
select(GeneID, GeneType, Description, Orthogroup, Tissue, Species, Status) # Ensure Species column is included
# Combine results
summary_table <- bind_rows(summary_table, head_merged, thorax_merged)
}
# Pivot table to show Up/Down/Not Significant per species
summary_table_pivot <- summary_table %>%
pivot_wider(names_from = c(Species, Tissue), values_from = Status, values_fill = "Not Detected")
# Create a searchable DataTable with color formatting
datatable(
summary_table_pivot,
options = list(
pageLength = 50, # Show only the first 50 rows by default
scrollX = TRUE, # Enable horizontal scrolling if needed
autoWidth = TRUE, # Adjust column width automatically
searchHighlight = TRUE # Highlight search results
),
rownames = FALSE,
class = "compact" # Applies a smaller font size
) %>%
formatStyle(
columns = names(summary_table_pivot)[-c(1,2)], # Exclude Orthogroup and GeneID from color formatting
backgroundColor = styleEqual(
c("Upregulated", "Downregulated"),
c("lightcoral", "lightblue") # Red for Upregulated, Blue for Downregulated
),
color = styleEqual(
c("Upregulated", "Downregulated"),
c("white", "black") # White text for Upregulated, Black text for Downregulated
)
)# Save as CSV
output_file <- file.path(workDir, "overlap/summaryPolyneoptera_DEGs_Orthogroups_togregaria_Feb2025.csv")
write.csv(summary_table_pivot, output_file, row.names = FALSE)
message(paste("Summary table saved at:", output_file))This table summarize the DEGs as well as the orthogroups it belongs using the DEGs mapped to own RefSeq.
library(tidyverse)
# Load Orthogroup information
ortho_dir <- "/Users/maevatecher/Documents/GitHub/locust-comparative-genomics/data/orthofinder/Polyneoptera"
input_file <- file.path(ortho_dir, "Results_I2/Orthogroups_genesproteinbiotype_13species_Jan2025.csv")
ortholog_df <- read_csv(input_file, trim_ws = TRUE)
# Replace NA values in the Orthogroup column with "Unassigned"
ortholog_df$Orthogroup[is.na(ortholog_df$Orthogroup)] <- "Unassigned"
# Ensure correct column names
if ("gene_id" %in% colnames(ortholog_df)) {
colnames(ortholog_df)[colnames(ortholog_df) == "gene_id"] <- "GeneID"
}
# Keep only relevant columns and ensure uniqueness
ortholog_df <- ortholog_df %>%
select(GeneID, GeneType, Orthogroup, Description, Species) %>%
distinct(GeneID, .keep_all = TRUE)
# Define species list
species_list <- c("gregaria", "piceifrons", "cancellata", "americana", "cubense", "nitens")
# Initialize an empty data frame for summary
summary_table <- data.frame()
# Loop through each species
for (species in species_list) {
message(paste("Processing:", species))
# Load DESeq2 results for Head and Thorax
head_file <- file.path(workDir, "DEG_results/Bulk_RNAseq", paste0("DESeq2_sigresults_Head_", species, ".csv"))
thorax_file <- file.path(workDir, "DEG_results/Bulk_RNAseq", paste0("DESeq2_sigresults_Thorax_", species, ".csv"))
# Check if files exist
if (!file.exists(head_file) || !file.exists(thorax_file)) {
message(paste("Missing DESeq2 results for:", species))
next
}
head_data <- read.csv(head_file, stringsAsFactors = FALSE)
thorax_data <- read.csv(thorax_file, stringsAsFactors = FALSE)
# Ensure GeneID column exists
if (!"GeneID" %in% colnames(head_data) && "X" %in% colnames(head_data)) {
colnames(head_data)[colnames(head_data) == "X"] <- "GeneID"
}
if (!"GeneID" %in% colnames(thorax_data) && "X" %in% colnames(thorax_data)) {
colnames(thorax_data)[colnames(thorax_data) == "X"] <- "GeneID"
}
# Convert GeneID to character
head_data$GeneID <- as.character(head_data$GeneID)
thorax_data$GeneID <- as.character(thorax_data$GeneID)
ortholog_df$GeneID <- as.character(ortholog_df$GeneID)
# Merge with Orthogroups and ensure Orthogroup is always character
head_merged <- left_join(head_data, ortholog_df, by = "GeneID") %>%
mutate(Orthogroup = as.character(ifelse(is.na(Orthogroup), "Unassigned", Orthogroup)))
thorax_merged <- left_join(thorax_data, ortholog_df, by = "GeneID") %>%
mutate(Orthogroup = as.character(ifelse(is.na(Orthogroup), "Unassigned", Orthogroup)))
# Classify DEGs and add Tissue + Species columns
head_merged <- head_merged %>%
mutate(
Status = case_when(
padj < 0.05 & log2FoldChange > 1 ~ "Upregulated",
padj < 0.05 & log2FoldChange < -1 ~ "Downregulated",
TRUE ~ "Not Significant"
),
Tissue = "Head", # Add Tissue column
Species = species # Add Species column (Fix!)
) %>%
select(GeneID, GeneType, Description, Orthogroup, Tissue, Species, Status) # Ensure Species column is included
thorax_merged <- thorax_merged %>%
mutate(
Status = case_when(
padj < 0.05 & log2FoldChange > 1 ~ "Upregulated",
padj < 0.05 & log2FoldChange < -1 ~ "Downregulated",
TRUE ~ "Not Significant"
),
Tissue = "Thorax", # Add Tissue column
Species = species # Add Species column (Fix!)
) %>%
select(GeneID, GeneType, Description, Orthogroup, Tissue, Species, Status) # Ensure Species column is included
# Combine results
summary_table <- bind_rows(summary_table, head_merged, thorax_merged)
}
# Pivot table to show Up/Down/Not Significant per species
summary_table_pivot <- summary_table %>%
pivot_wider(names_from = c(Species, Tissue), values_from = Status, values_fill = "Not Detected")
# Create a searchable DataTable with color formatting
datatable(
summary_table_pivot,
options = list(
pageLength = 50, # Show only the first 50 rows by default
scrollX = TRUE, # Enable horizontal scrolling if needed
autoWidth = TRUE, # Adjust column width automatically
searchHighlight = TRUE # Highlight search results
),
rownames = FALSE,
class = "compact" # Applies a smaller font size
) %>%
formatStyle(
columns = names(summary_table_pivot)[-c(1,2)], # Exclude Orthogroup and GeneID from color formatting
backgroundColor = styleEqual(
c("Upregulated", "Downregulated"),
c("lightcoral", "lightblue") # Red for Upregulated, Blue for Downregulated
),
color = styleEqual(
c("Upregulated", "Downregulated"),
c("white", "black") # White text for Upregulated, Black text for Downregulated
)
)# Save as CSV
output_file <- file.path(workDir, "overlap/summaryPolyneoptera_DEGs_Orthogroups_Feb2025.csv")
write.csv(summary_table_pivot, output_file, row.names = FALSE)
message(paste("Summary table saved at:", output_file))
sessionInfo()R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS 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] DT_0.33 kableExtra_1.4.0 lubridate_1.9.4 ggplot2_3.5.1
[5] tidyverse_2.0.0 forcats_1.0.0 tibble_3.2.1 purrr_1.0.4
[9] stringr_1.5.1 readr_2.1.5 tidyr_1.3.1 dplyr_1.1.4
loaded via a namespace (and not attached):
[1] sass_0.4.9 generics_0.1.3 xml2_1.3.6 stringi_1.8.4
[5] hms_1.1.3 digest_0.6.37 magrittr_2.0.3 evaluate_1.0.3
[9] grid_4.4.1 timechange_0.3.0 fastmap_1.2.0 rprojroot_2.0.4
[13] workflowr_1.7.1 jsonlite_1.8.9 promises_1.3.2 crosstalk_1.2.1
[17] viridisLite_0.4.2 scales_1.3.0 jquerylib_0.1.4 cli_3.6.3
[21] crayon_1.5.3 rlang_1.1.5 bit64_4.6.0-1 munsell_0.5.1
[25] withr_3.0.2 cachem_1.1.0 yaml_2.3.10 parallel_4.4.1
[29] tools_4.4.1 tzdb_0.4.0 colorspace_2.1-1 httpuv_1.6.15
[33] vctrs_0.6.5 R6_2.5.1 lifecycle_1.0.4 git2r_0.35.0
[37] bit_4.5.0.1 htmlwidgets_1.6.4 fs_1.6.5 vroom_1.6.5
[41] pkgconfig_2.0.3 pillar_1.10.1 bslib_0.9.0 later_1.4.1
[45] gtable_0.3.6 glue_1.8.0 Rcpp_1.0.14 systemfonts_1.2.1
[49] xfun_0.50 tidyselect_1.2.1 rstudioapi_0.17.1 knitr_1.49
[53] htmltools_0.5.8.1 rmarkdown_2.29 svglite_2.1.3 compiler_4.4.1