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Filtering and Analysis/Metabarcoding_Filtering_Analysis/usearch_data/CSIRO_hives_all_otu97_taxonomy_ITS2_minsize8_80pc.csv
Filtering and Analysis/RNASeq_Filtering_Analysis/figures/._Figure7.pdf
Filtering and Analysis/Metabarcoding_Filtering_Analysis/usearch_data/._CSIRO_hives_all_otu97_taxonomy_pivotCOI_minsize8_90pc.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/._metabarcoding_cleanup_CSIRO_hives.pdf
Filtering and Analysis/Metabarcoding_Filtering_Analysis/usearch_data/CSIRO_hives_all_zotu_taxonomy_pivot16S_minsize8_90pc.csv
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Filtering and Analysis/RNASeq_Filtering_Analysis/figures/._FigS4.pdf
Filtering and Analysis/Metabarcoding_Filtering_Analysis/.DS_Store
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Filtering and Analysis/RNASeq_Filtering_Analysis/contig_lengths.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/usearch_data/CSIRO_hives_all_otu97_taxonomy_pivotITS2_minsize8_80pc.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/clean_data/ITS_fungi_function_query.txt
Filtering and Analysis/Metabarcoding_Filtering_Analysis/usearch_data/._CSIRO_hives_all_otu97_taxonomy_COI_minsize8_90pc.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/clean_data/._ITS_taxa_table_90pc.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/Hive eDNA sample types datasheet.xlsx
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Filtering and Analysis/Metabarcoding_Filtering_Analysis/usearch_data/CSIRO_hives_all_otu97_taxonomy_ITS2_minsize8_90pc.csv
Filtering and Analysis/RNASeq_Filtering_Analysis/taxonomy_list_filtered_reads.csv
Filtering and Analysis/RNASeq_Filtering_Analysis/._RNA_analysis.Rmd
Filtering and Analysis/Metabarcoding_Filtering_Analysis/._t_test_comparisons.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/figures/._FigS2.pdf
Filtering and Analysis/Metabarcoding_Filtering_Analysis/usearch_data/CSIRO_hives_all_otu97_taxonomy_ITS_minsize8_90pc.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/figures/._Figure4.pdf
Filtering and Analysis/RNASeq_Filtering_Analysis/._otu_read_counts_NEW.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/usearch_data/._CSIRO_hives_all_zotu_taxonomy_16S_minsize8_80pc_RDP.csv
Filtering and Analysis/RNASeq_Filtering_Analysis/RNA_filtering.Rmd
Filtering and Analysis/RNASeq_Filtering_Analysis/RNA_analysis.Rmd
Filtering and Analysis/Metabarcoding_Filtering_Analysis/clean_data/CSIRO_hives_16S_90pc.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/usearch_data/CSIRO_hives_all_otu97_taxonomy_pivotCOI_minsize8_90pc.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/clean_data/._CSIRO_hives_COI_90pc.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/clean_data/CSIRO_hives_COI_90pc.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/usearch_data/._CSIRO_hives_all_zotu_taxonomy_pivot16S_minsize8_80pc_RDP.csv
Filtering and Analysis/RNASeq_Filtering_Analysis/figures/._Figure9.pdf
Filtering and Analysis/Metabarcoding_Filtering_Analysis/usearch_data/._CSIRO_hives_all_otu97_taxonomy_ITS2_minsize8_90pc.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/clean_data/._CSIRO_hives_ITS2_90pc.csv
Filtering and Analysis/RNASeq_Filtering_Analysis/RNA_filtering.pdf
Filtering and Analysis/Metabarcoding_Filtering_Analysis/figures/._Figure3.pdf
Filtering and Analysis/Metabarcoding_Filtering_Analysis/metabarcoding_analysis_CSIRO_hives.pdf
Filtering and Analysis/RNASeq_Filtering_Analysis/otu_read_counts_NEW.csv
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Filtering and Analysis/Metabarcoding_Filtering_Analysis/clean_data/._ITS_fungi_function_query.txt
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Filtering and Analysis/Metabarcoding_Filtering_Analysis/clean_data/._ITS2_taxa_table_90pc.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/clean_data/ITS_fungi_function_query.guilds_matched.txt
Filtering and Analysis/Metabarcoding_Filtering_Analysis/._usearch_data
Filtering and Analysis/Metabarcoding_Filtering_Analysis/clean_data/._CSIRO_hives_ITS_90pc.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/usearch_data/CSIRO_hives_all_zotu_taxonomy_pivot16S_minsize8_80pc.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/usearch_data/._CSIRO_hives_all_otu97_taxonomy_COI_minsize8_80pc.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/decon.diff.modified.R
Filtering and Analysis/RNASeq_Filtering_Analysis/._RNA_filtering.pdf
Filtering and Analysis/Metabarcoding_Filtering_Analysis/clean_data/ITS2_taxa_table_90pc.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/clean_data/COI_taxa_table_90pc.csv
Filtering and Analysis/RNASeq_Filtering_Analysis/combined_virusall_sums_contig_lengths.csv
Filtering and Analysis/RNASeq_Filtering_Analysis/._taxonomy_list_filtered_reads.csv
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Filtering and Analysis/Metabarcoding_Filtering_Analysis/usearch_data/CSIRO_hives_all_otu97_taxonomy_pivotITS2_minsize8_90pc.csv
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Filtering and Analysis/Metabarcoding_Filtering_Analysis/usearch_data/._CSIRO_hives_all_zotu_taxonomy_16S_minsize8_80pc.csv
Raw data files, analysis scripts and input files to generate data presented in the manuscript
Surface swabs outperform most traditional honeybee (Apis mellifera) hive samples for recovery of eDNA and eRNA
Filtering and Analysis/RNASeq_Filtering_Analysis/._RNA_analysis.pdf
Filtering and Analysis/Metabarcoding_Filtering_Analysis/figures/._FigS1.pdf
Filtering and Analysis/RNASeq_Filtering_Analysis/figures/._FigS3.pdf
Filtering and Analysis/Metabarcoding_Filtering_Analysis/usearch_data/._CSIRO_hives_all_otu97_taxonomy_pivotITS2_minsize8_80pc.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/metabarcoding_cleanup_CSIRO_hives.Rmd
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Filtering and Analysis/Metabarcoding_Filtering_Analysis/t_test_comparisons.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/metabarcoding_cleanup_CSIRO_hives.pdf
Filtering and Analysis/Metabarcoding_Filtering_Analysis/figures/._Figure5.pdf
Filtering and Analysis/Metabarcoding_Filtering_Analysis/usearch_data/._CSIRO_hives_all_zotu_taxonomy_pivot16S_minsize8_90pc.csv
Filtering and Analysis/RNASeq_Filtering_Analysis/RNA_filtered_contigs_PhyloSeq.rds
Filtering and Analysis/Metabarcoding_Filtering_Analysis/clean_data/16S_taxa_table_90pc.csv
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Filtering and Analysis/Metabarcoding_Filtering_Analysis/usearch_data/CSIRO_hives_all_zotu_taxonomy_pivot16S_minsize8_80pc_RDP.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/clean_data/CSIRO_hives_ITS_90pc.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/usearch_data/CSIRO_hives_all_zotu_taxonomy_16S_minsize8_80pc.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/metabarcoding_analysis_CSIRO_hives.Rmd
Filtering and Analysis/RNASeq_Filtering_Analysis/._RNA_filtering.Rmd
Filtering and Analysis/Metabarcoding_Filtering_Analysis/clean_data/CSIRO_hives_ITS2_90pc.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/clean_data/._16S_taxa_table_90pc.csv
Filtering and Analysis/RNASeq_Filtering_Analysis/taxonomy_list_filtered_contigs_NEW.csv
Raw Files/fastq_files_RNA_sequencing.zip
Filtering and Analysis/Metabarcoding_Filtering_Analysis/._metabarcoding_cleanup_CSIRO_hives.Rmd
Filtering and Analysis/Metabarcoding_Filtering_Analysis/._decon.diff.modified.R
Filtering and Analysis/RNASeq_Filtering_Analysis/gather_summary_files_R_environment.Rdata
Filtering and Analysis/Metabarcoding_Filtering_Analysis/figures/._Figure2.pdf
Filtering and Analysis/Metabarcoding_Filtering_Analysis/usearch_data/CSIRO_hives_all_otu97_taxonomy_pivotITS_minsize8_90pc.csv
Filtering and Analysis/RNASeq_Filtering_Analysis/figures/._Figure6.pdf
Filtering and Analysis/Metabarcoding_Filtering_Analysis/usearch_data/._CSIRO_hives_all_zotu_taxonomy_pivot16S_minsize8_80pc.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/clean_data/._CSIRO_hives_16S_90pc.csv
Filtering and Analysis/RNASeq_Filtering_Analysis/._.DS_Store
Filtering and Analysis/Metabarcoding_Filtering_Analysis/usearch_data/CSIRO_hives_all_zotu_taxonomy_16S_minsize8_80pc_RDP.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/usearch_data/CSIRO_hives_all_otu97_taxonomy_ITS_minsize8_80pc.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/clean_data/._ITS_fungi_function_query.guilds_matched.txt
Filtering and Analysis/Metabarcoding_Filtering_Analysis/clean_data/ITS_taxa_table_90pc.csv
Filtering and Analysis/RNASeq_Filtering_Analysis/._contig_lengths.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/usearch_data/CSIRO_hives_all_otu97_taxonomy_pivotITS_minsize8_80pc.csv
Filtering and Analysis/RNASeq_Filtering_Analysis/._RNA_total_reads_by_species.csv
Filtering and Analysis/RNASeq_Filtering_Analysis/._taxonomy_list_filtered_contigs_NEW.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/figures/._Figure1.pdf
Filtering and Analysis/RNASeq_Filtering_Analysis/.DS_Store
Filtering and Analysis/Metabarcoding_Filtering_Analysis/usearch_data/._CSIRO_hives_all_otu97_taxonomy_ITS2_minsize8_80pc.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/usearch_data/CSIRO_hives_all_otu97_taxonomy_pivotCOI_minsize8_80pc.csv
Filtering and Analysis/RNASeq_Filtering_Analysis/figures/._Figure8.pdf
Filtering and Analysis/Metabarcoding_Filtering_Analysis/usearch_data/._CSIRO_hives_all_otu97_taxonomy_ITS_minsize8_80pc.csv
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Filtering and Analysis/Metabarcoding_Filtering_Analysis/._clean_data
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Filtering and Analysis/RNASeq_Filtering_Analysis/RNA_analysis.pdf
Filtering and Analysis/Metabarcoding_Filtering_Analysis/usearch_data/CSIRO_hives_all_zotu_taxonomy_16S_minsize8_90pc.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/usearch_data/._CSIRO_hives_all_zotu_taxonomy_16S_minsize8_90pc.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/clean_data/._COI_taxa_table_90pc.csv
Filtering and Analysis/Metabarcoding_Filtering_Analysis/._metabarcoding_analysis_CSIRO_hives.pdf
Filtering and Analysis/RNASeq_Filtering_Analysis/._RNA_filtered_contigs_PhyloSeq.rds
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