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  1. mikropml::otu_data_preproc
    Mini OTU abundance dataset - preprocessed
    json| rda| rds
    list
  2. mikropml::otu_mini_bin
    Mini OTU abundance dataset
    csv| xlsx| json| ndjson| rda| rds
    data.frame|200 x 11
  3. mikropml::otu_mini_bin_results_glmnet
    Results from running the pipeline with L2 logistic regression on 'otu_mini_bin' with feature importance and grouping
    rda| rds
    list
  4. mikropml::otu_mini_bin_results_rf
    Results from running the pipeline with random forest on 'otu_mini_bin'
    rda| rds
    list
  5. mikropml::otu_mini_bin_results_rpart2
    Results from running the pipeline with rpart2 on 'otu_mini_bin'
    rda| rds
    list
  6. mikropml::otu_mini_bin_results_svmRadial
    Results from running the pipeline with svmRadial on 'otu_mini_bin'
    rda| rds
    list
  7. mikropml::otu_mini_bin_results_xgbTree
    Results from running the pipeline with xbgTree on 'otu_mini_bin'
    rda| rds
    list
  8. mikropml::otu_mini_cont_results_glmnet
    Results from running the pipeline with glmnet on 'otu_mini_bin' with 'Otu00001' as the outcome
    rda| rds
    list
  9. mikropml::otu_mini_cont_results_nocv
    Results from running the pipeline with glmnet on 'otu_mini_bin' with 'Otu00001' as the outcome column, using a custom train control scheme that does not perform cross-validation
    rda| rds
    list
  10. mikropml::otu_mini_cv
    Cross validation on 'train_data_mini' with grouped features.
    json| rda| rds
    list
  11. mikropml::otu_mini_multi
    Mini OTU abundance dataset with 3 categorical variables
    csv| xlsx| json| ndjson| rda| rds
    data.frame|490 x 11
  12. mikropml::otu_mini_multi_group
    Groups for otu_mini_multi
    json| rda| rds
    character
  13. mikropml::otu_mini_multi_results_glmnet
    Results from running the pipeline with glmnet on 'otu_mini_multi' for multiclass outcomes
    rda| rds
    list
  14. mikropml::otu_small
    Small OTU abundance dataset
    csv| xlsx| json| ndjson| rda| rds
    data.frame|200 x 61
  15. mikropml::otu_data_preproc
    Mini OTU abundance dataset - preprocessed
    json| rda| rds
    list
  16. mikropml::otu_mini_bin
    Mini OTU abundance dataset
    csv| xlsx| json| ndjson| rda| rds
    data.frame|200 x 11
  17. mikropml::otu_mini_bin_results_glmnet
    Results from running the pipeline with L2 logistic regression on 'otu_mini_bin' with feature importance and grouping
    rda| rds
    list
  18. mikropml::otu_mini_bin_results_rf
    Results from running the pipeline with random forest on 'otu_mini_bin'
    rda| rds
    list
  19. mikropml::otu_mini_bin_results_rpart2
    Results from running the pipeline with rpart2 on 'otu_mini_bin'
    rda| rds
    list
  20. mikropml::otu_mini_bin_results_svmRadial
    Results from running the pipeline with svmRadial on 'otu_mini_bin'
    rda| rds
    list
  21. mikropml::otu_mini_bin_results_xgbTree
    Results from running the pipeline with xbgTree on 'otu_mini_bin'
    rda| rds
    list
  22. mikropml::otu_mini_cont_results_glmnet
    Results from running the pipeline with glmnet on 'otu_mini_bin' with 'Otu00001' as the outcome
    rda| rds
    list
  23. mikropml::otu_mini_cont_results_nocv
    Results from running the pipeline with glmnet on 'otu_mini_bin' with 'Otu00001' as the outcome column, using a custom train control scheme that does not perform cross-validation
    rda| rds
    list
  24. mikropml::otu_mini_cv
    Cross validation on 'train_data_mini' with grouped features.
    json| rda| rds
    list
  25. mikropml::otu_mini_multi
    Mini OTU abundance dataset with 3 categorical variables
    csv| xlsx| json| ndjson| rda| rds
    data.frame|490 x 11
  26. mikropml::otu_mini_multi_group
    Groups for otu_mini_multi
    json| rda| rds
    character
  27. mikropml::otu_mini_multi_results_glmnet
    Results from running the pipeline with glmnet on 'otu_mini_multi' for multiclass outcomes
    rda| rds
    list
  28. mikropml::otu_small
    Small OTU abundance dataset
    csv| xlsx| json| ndjson| rda| rds
    data.frame|200 x 61
  29. MOSuite::gene_counts
    RSEM expected gene counts
    csv| xlsx| json| ndjson| rda| rds
    spec_tbl_df|58929 x 6
  30. MOSuite::nidap_batch_corrected_counts
    Batch-corrected counts for the NIDAP test dataset.
    csv| xlsx| json| ndjson| rda| rds
    spec_tbl_df|7943 x 10
  31. MOSuite::nidap_batch_corrected_counts_2
    Batch-corrected counts for the NIDAP test dataset. The result of running 'batch_correct_counts()' on 'nidap_norm_counts'.
    csv| xlsx| json| ndjson| rda| rds
    data.frame|7943 x 10
  32. MOSuite::nidap_clean_raw_counts
    Clean raw counts for the NIDAP test dataset. The result of running 'clean_raw_counts()' on 'nidap_raw_counts'.
    csv| xlsx| json| ndjson| rda| rds
    spec_tbl_df|43280 x 10
  33. MOSuite::nidap_deg_analysis
    Differential gene expression analysis for the NIDAP test dataset.
    csv| xlsx| json| ndjson| rda| rds
    spec_tbl_df|7943 x 25
  34. MOSuite::nidap_deg_analysis_2
    Differential gene expression analysis for the NIDAP test dataset. The result of running 'diff_counts()' on 'nidap_filtered_counts'.
    csv| json| rda| rds
    list
  35. MOSuite::nidap_deg_gene_list
    List of differentially expressed genes from the NIDAP test dataset using default parameters with 'filter_diff()'.
    csv| xlsx| json| ndjson| rda| rds
    data.frame|641 x 16
  36. MOSuite::nidap_filtered_counts
    Filtered counts for the NIDAP test dataset. The result of running 'filter_counts()' on 'nidap_clean_raw_counts'.
    csv| xlsx| json| ndjson| rda| rds
    spec_tbl_df|7943 x 10
  37. MOSuite::nidap_norm_counts
    Normalized counts for the NIDAP test dataset. The result of running 'normalize_counts()' on 'nidap_filtered_counts'.
    csv| xlsx| json| ndjson| rda| rds
    spec_tbl_df|7943 x 10
  38. MOSuite::nidap_raw_counts
    Raw counts for the NIDAP test dataset Pairs with 'nidap_sample_metadata'.
    csv| xlsx| json| ndjson| rda| rds
    spec_tbl_df|43280 x 10
  39. MOSuite::nidap_sample_metadata
    Sample metadata for the NIDAP test dataset
    csv| xlsx| json| ndjson| rda| rds
    spec_tbl_df|9 x 5
  40. MOSuite::nidap_venn_diagram_dat
    Output data from venn diagram. The result of running 'plot_venn_diagram()' on 'nidap_volcano_summary_dat'
    csv| xlsx| json| ndjson| rda| rds
    spec_tbl_df|3068 x 4
  41. MOSuite::nidap_volcano_summary_dat
    Summarized differential expression analysis for input to venn diagram
    csv| xlsx| json| ndjson| rda| rds
    spec_tbl_df|4929 x 7
  42. MOSuite::gene_counts
    RSEM expected gene counts
    csv| xlsx| json| ndjson| rda| rds
    spec_tbl_df|58929 x 6
  43. MOSuite::nidap_batch_corrected_counts
    Batch-corrected counts for the NIDAP test dataset.
    csv| xlsx| json| ndjson| rda| rds
    spec_tbl_df|7943 x 10
  44. MOSuite::nidap_batch_corrected_counts_2
    Batch-corrected counts for the NIDAP test dataset. The result of running 'batch_correct_counts()' on 'nidap_norm_counts'.
    csv| xlsx| json| ndjson| rda| rds
    data.frame|7943 x 10
  45. MOSuite::nidap_clean_raw_counts
    Clean raw counts for the NIDAP test dataset. The result of running 'clean_raw_counts()' on 'nidap_raw_counts'.
    csv| xlsx| json| ndjson| rda| rds
    spec_tbl_df|43280 x 10
  46. MOSuite::nidap_deg_analysis
    Differential gene expression analysis for the NIDAP test dataset.
    csv| xlsx| json| ndjson| rda| rds
    spec_tbl_df|7943 x 25
  47. MOSuite::nidap_deg_analysis_2
    Differential gene expression analysis for the NIDAP test dataset. The result of running 'diff_counts()' on 'nidap_filtered_counts'.
    csv| json| rda| rds
    list
  48. MOSuite::nidap_deg_gene_list
    List of differentially expressed genes from the NIDAP test dataset using default parameters with 'filter_diff()'.
    csv| xlsx| json| ndjson| rda| rds
    data.frame|641 x 16
  49. MOSuite::nidap_filtered_counts
    Filtered counts for the NIDAP test dataset. The result of running 'filter_counts()' on 'nidap_clean_raw_counts'.
    csv| xlsx| json| ndjson| rda| rds
    spec_tbl_df|7943 x 10
  50. MOSuite::nidap_norm_counts
    Normalized counts for the NIDAP test dataset. The result of running 'normalize_counts()' on 'nidap_filtered_counts'.
    csv| xlsx| json| ndjson| rda| rds
    spec_tbl_df|7943 x 10
  51. MOSuite::nidap_raw_counts
    Raw counts for the NIDAP test dataset Pairs with 'nidap_sample_metadata'.
    csv| xlsx| json| ndjson| rda| rds
    spec_tbl_df|43280 x 10
  52. MOSuite::nidap_sample_metadata
    Sample metadata for the NIDAP test dataset
    csv| xlsx| json| ndjson| rda| rds
    spec_tbl_df|9 x 5
  53. MOSuite::nidap_venn_diagram_dat
    Output data from venn diagram. The result of running 'plot_venn_diagram()' on 'nidap_volcano_summary_dat'
    csv| xlsx| json| ndjson| rda| rds
    spec_tbl_df|3068 x 4
  54. MOSuite::nidap_volcano_summary_dat
    Summarized differential expression analysis for input to venn diagram
    csv| xlsx| json| ndjson| rda| rds
    spec_tbl_df|4929 x 7