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

Folder: qiime

d .. (parent)
d d rwxr-xr-x 4,096 denoiser
d d rwxr-xr-x 4,096 parallel
d d rwxr-xr-x 51 pycogent_backports
d d rwxr-xr-x 126 support_files
d d rwxr-xr-x 4,096 workflow
- - rw-r--r-- 1,463 __init__.py
- - rwxr-xr-x 8,635 add_alpha_to_mapping_file.py
- - rwxr-xr-x 5,376 add_qiime_labels.py
- - rwxr-xr-x 1,572 adjust_seq_orientation.py
- - rw-r--r-- 11,365 align_seqs.py
- - rw-r--r-- 15,169 alpha_diversity.py
- - rw-r--r-- 56,699 assign_taxonomy.py
- - rw-r--r-- 3,684 barcode.py
- - rw-r--r-- 10,483 beta_diversity.py
- - rw-r--r-- 8,285 beta_metrics.py
- - rw-r--r-- 5,457 biplots.py
- - rwxr-xr-x 2,480 categorized_dist_scatterplot.py
- - rw-r--r-- 39,157 check_id_map.py
- - rw-r--r-- 2,660 clean_raxml_parsimony_tree.py
- - rw-r--r-- 1,257 cluster_quality.py
- - rw-r--r-- 2,343 collate_alpha.py
- - rw-r--r-- 24,387 colors.py
- - rw-r--r-- 11,923 compare_alpha_diversity.py
- - rwxr-xr-x 7,127 compare_categories.py
- - rwxr-xr-x 11,255 compare_distance_matrices.py
- - rwxr-xr-x 25,490 compare_taxa_summaries.py
- - rw-r--r-- 3,740 compare_trajectories.py
- - rw-r--r-- 2,421 compute_taxonomy_ratios.py
- - rw-r--r-- 12,017 convert_fastaqual_fastq.py
- - rw-r--r-- 3,320 core_microbiome.py
- - rwxr-xr-x 34,937 demultiplex_fasta.py
- - rw-r--r-- 2,149 denoise_wrapper.py
- - rw-r--r-- 6,114 detrend.py
- - rwxr-xr-x 7,886 differential_abundance.py
- - rw-r--r-- 5,829 distance_matrix_from_mapping.py
- - rwxr-xr-x 20,679 estimate_observation_richness.py
- - rw-r--r-- 11,966 exclude_seqs_by_blast.py
- - rw-r--r-- 24,819 extract_barcodes.py
- - rw-r--r-- 26,095 filter.py
- - rwxr-xr-x 6,366 filter_alignment.py
- - rw-r--r-- 4,492 filter_otus_by_sample.py
- - rwxr-xr-x 37,800 format.py
- - rw-r--r-- 7,943 golay.py
- - rwxr-xr-x 35,015 group.py
- - rw-r--r-- 5,067 hamming.py
- - rw-r--r-- 2,599 hierarchical_cluster.py
- - rwxr-xr-x 46,965 identify_chimeric_seqs.py
- - rw-r--r-- 3,280 join_paired_ends.py
- - rw-r--r-- 23,536 make_2d_plots.py
- - rw-r--r-- 11,256 make_bipartite_network.py
- - rw-r--r-- 1,348 make_bootstrapped_tree.py
- - rwxr-xr-x 12,393 make_distance_boxplots.py
- - rw-r--r-- 3,279 make_fastq.py
- - rw-r--r-- 1,320 make_library_id_lists.py
- - rw-r--r-- 7,167 make_otu_heatmap.py
- - rw-r--r-- 57,299 make_otu_network.py
- - rw-r--r-- 3,734 make_otu_table.py
- - rw-r--r-- 3,545 make_per_library_sff.py
- - rw-r--r-- 9,015 make_phylogeny.py
- - rw-r--r-- 65,383 make_rarefaction_plots.py
- - rw-r--r-- 14,824 map_reads_to_reference.py
- - rw-r--r-- 1,413 nmds.py
- - rwxr-xr-x 5,178 normalize_table.py
- - rw-r--r-- 17,807 otu_significance.py
- - rw-r--r-- 32,177 parse.py
- - rw-r--r-- 82,383 pick_otus.py
- - rw-r--r-- 14,139 pick_rep_set.py
- - rw-r--r-- 4,171 plot_rank_abundance_graph.py
- - rw-r--r-- 5,404 plot_semivariogram.py
- - rw-r--r-- 44,244 plot_taxa_summary.py
- - rw-r--r-- 761 principal_coordinates.py
- - rw-r--r-- 9,705 process_sff.py
- - rwxr-xr-x 6,914 quality_scores_plot.py
- - rw-r--r-- 6,791 rarefaction.py
- - rw-r--r-- 6,833 relatedness_library.py
- - rwxr-xr-x 13,008 remote.py
- - rw-r--r-- 2,746 shared_phylotypes.py
- - rwxr-xr-x 11,757 simsam.py
- - rw-r--r-- 7,365 sort.py
- - rw-r--r-- 8,492 split.py
- - rw-r--r-- 62,176 split_libraries.py
- - rw-r--r-- 17,992 split_libraries_fastq.py
- - rw-r--r-- 28,236 split_libraries_lea_seq.py
- - rw-r--r-- 92,598 stats.py
- - rw-r--r-- 5,580 summarize_taxa.py
- - rw-r--r-- 9,543 supervised_learning.py
- - rw-r--r-- 115,074 test.py
- - rw-r--r-- 10,592 transform_coordinate_matrices.py
- - rw-r--r-- 9,046 tree_compare.py
- - rw-r--r-- 5,934 trim_sff_primers.py
- - rwxr-xr-x 6,319 truncate_fasta_qual_files.py
- - rwxr-xr-x 7,045 truncate_reverse_primer.py
- - rw-r--r-- 76,509 util.py
- - rwxr-xr-x 20,191 validate_demultiplexed_fasta.py