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qiime 1.9.1+dfsg-3
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  • size: 114,512 kB
  • sloc: python: 109,265; haskell: 379; makefile: 127; sh: 107

Folder: qiime_test_data

d .. (parent)
d d rwxr-xr-x 96 add_alpha_to_mapping_file
d d rwxr-xr-x 60 add_qiime_labels
d d rwxr-xr-x 51 adjust_seq_orientation
d d rwxr-xr-x 4,096 align_seqs
d d rwxr-xr-x 78 alpha_diversity
d d rwxr-xr-x 67 alpha_rarefaction
d d rwxr-xr-x 58 ampliconnoise
d d rwxr-xr-x 4,096 assign_taxonomy
d d rwxr-xr-x 78 beta_diversity
d d rwxr-xr-x 67 beta_diversity_through_plots
d d rwxr-xr-x 45 beta_significance
d d rwxr-xr-x 57 blast_wrapper
d d rwxr-xr-x 135 cluster_quality
d d rwxr-xr-x 49 collapse_samples
d d rwxr-xr-x 22 collate_alpha
d d rwxr-xr-x 48 compare_alpha_diversity
d d rwxr-xr-x 72 compare_categories
d d rwxr-xr-x 4,096 compare_distance_matrices
d d rwxr-xr-x 124 compare_taxa_summaries
d d rwxr-xr-x 51 compare_trajectories
d d rwxr-xr-x 70 compute_core_microbiome
d d rwxr-xr-x 40 compute_taxonomy_ratios
d d rwxr-xr-x 35 conditional_uncovered_probability
d d rwxr-xr-x 37 consensus_tree
d d rwxr-xr-x 70 convert_fastaqual_fastq
d d rwxr-xr-x 59 core_diversity_analyses
d d rwxr-xr-x 69 count_seqs
d d rwxr-xr-x 4,096 demultiplex_fasta
d d rwxr-xr-x 85 denoiser_preprocess
d d rwxr-xr-x 74 differential_abundance
d d rwxr-xr-x 26 dissimilarity_mtx_stats
d d rwxr-xr-x 93 distance_matrix_from_mapping
d d rwxr-xr-x 35 estimate_observation_richness
d d rwxr-xr-x 66 exclude_seqs_by_blast
d d rwxr-xr-x 35 extract_reads_from_interleaved_file
d d rwxr-xr-x 39 extract_seqs_by_sample_id
d d rwxr-xr-x 83 filter_alignment
d d rwxr-xr-x 107 filter_distance_matrix
d d rwxr-xr-x 4,096 filter_fasta
d d rwxr-xr-x 41 filter_otus_by_sample
d d rwxr-xr-x 51 filter_otus_from_otu_table
d d rwxr-xr-x 71 filter_samples_from_otu_table
d d rwxr-xr-x 35 filter_taxa_from_otu_table
d d rwxr-xr-x 108 filter_tree
d d rwxr-xr-x 30 fix_arb_fasta
d d rwxr-xr-x 139 group_significance
d d rwxr-xr-x 4,096 identify_chimeric_seqs
d d rwxr-xr-x 31 identify_missing_files
d d rwxr-xr-x 53 identify_paired_differences
d d rwxr-xr-x 4,096 inflate_denoiser_output
d d rwxr-xr-x 83 jackknifed_beta_diversity
d d rwxr-xr-x 79 join_paired_ends
d d rwxr-xr-x 4,096 make_2d_plots
d d rwxr-xr-x 62 make_bipartite_network
d d rwxr-xr-x 68 make_bootstrapped_tree
d d rwxr-xr-x 72 make_distance_boxplots
d d rwxr-xr-x 85 make_distance_comparison_plots
d d rwxr-xr-x 4,096 make_fastq
d d rwxr-xr-x 84 make_otu_heatmap
d d rwxr-xr-x 61 make_otu_network
d d rwxr-xr-x 147 make_otu_table
d d rwxr-xr-x 44 make_phylogeny
d d rwxr-xr-x 47 make_prefs_file
d d rwxr-xr-x 85 make_rarefaction_plots
d d rwxr-xr-x 109 make_tep
d d rwxr-xr-x 4,096 map_reads_to_reference
d d rwxr-xr-x 51 merge_mapping_files
d d rwxr-xr-x 82 merge_otu_maps
d d rwxr-xr-x 62 merge_otu_tables
d d rwxr-xr-x 87 multiple_extract_barcodes
d d rwxr-xr-x 87 multiple_join_paired_ends
d d rwxr-xr-x 27 multiple_rarefactions
d d rwxr-xr-x 35 multiple_rarefactions_even_depth
d d rwxr-xr-x 123 multiple_split_libraries_fastq
d d rwxr-xr-x 69 neighbor_joining
d d rwxr-xr-x 69 nmds
d d rwxr-xr-x 56 normalize_table
d d rwxr-xr-x 53 observation_metadata_correlation
d d rwxr-xr-x 36 parallel_align_seqs_pynast
d d rwxr-xr-x 62 parallel_alpha_diversity
d d rwxr-xr-x 81 parallel_assign_taxonomy_blast
d d rwxr-xr-x 48 parallel_assign_taxonomy_rdp
d d rwxr-xr-x 25 parallel_assign_taxonomy_uclust
d d rwxr-xr-x 102 parallel_beta_diversity
d d rwxr-xr-x 72 parallel_blast
d d rwxr-xr-x 123 parallel_identify_chimeric_seqs
d d rwxr-xr-x 145 parallel_map_reads_to_reference
d d rwxr-xr-x 96 parallel_merge_otu_tables
d d rwxr-xr-x 50 parallel_multiple_rarefactions
d d rwxr-xr-x 51 parallel_pick_otus_blast
d d rwxr-xr-x 51 parallel_pick_otus_sortmerna
d d rwxr-xr-x 29 parallel_pick_otus_trie
d d rwxr-xr-x 39 parallel_pick_otus_uclust_ref
d d rwxr-xr-x 39 parallel_pick_otus_usearch61_ref
d d rwxr-xr-x 4,096 pick_closed_reference_otus
d d rwxr-xr-x 87 pick_de_novo_otus
d d rwxr-xr-x 153 pick_open_reference_otus
d d rwxr-xr-x 4,096 pick_otus
d d rwxr-xr-x 61 pick_rep_set
d d rwxr-xr-x 133 plot_rank_abundance_graph
d d rwxr-xr-x 4,096 plot_semivariogram
d d rwxr-xr-x 112 plot_taxa_summary
d d rwxr-xr-x 136 poller
d d rwxr-xr-x 57 principal_coordinates
d d rwxr-xr-x 32 print_metadata_stats
d d rwxr-xr-x 50 quality_scores_plot
d d rwxr-xr-x 60 relatedness
d d rwxr-xr-x 65 shared_phylotypes
d d rwxr-xr-x 59 simsam
d d rwxr-xr-x 35 single_rarefaction
d d rwxr-xr-x 90 sort_otu_table
d d rwxr-xr-x 4,096 split_libraries
d d rwxr-xr-x 156 split_libraries_fastq
d d rwxr-xr-x 56 split_libraries_lea_seq
d d rwxr-xr-x 49 split_otu_table
d d rwxr-xr-x 35 split_otu_table_by_taxonomy
d d rwxr-xr-x 50 split_sequence_file_on_sample_ids
d d rwxr-xr-x 34 start_parallel_jobs
d d rwxr-xr-x 34 start_parallel_jobs_sc
d d rwxr-xr-x 26 start_parallel_jobs_torque
d d rwxr-xr-x 21 subsample_fasta
d d rwxr-xr-x 61 summarize_taxa
d d rwxr-xr-x 61 summarize_taxa_through_plots
d d rwxr-xr-x 4,096 supervised_learning
d d rwxr-xr-x 4,096 transform_coordinate_matrices
d d rwxr-xr-x 59 tree_compare
d d rwxr-xr-x 33 trflp_file_to_otu_table
d d rwxr-xr-x 69 truncate_fasta_qual_files
d d rwxr-xr-x 67 truncate_reverse_primer
d d rwxr-xr-x 30 unweight_fasta
d d rwxr-xr-x 47 upgma_cluster
d d rwxr-xr-x 56 validate_mapping_file
- - rw-r--r-- 0 __init__.py