LICENSE
MANIFEST.in
README.md
history.md
readme.md
requirements.txt
setup.cfg
setup.py
examples/.metawibele.cfg.swp
examples/metawibele.cfg
examples/input/demo_genecatalogs.centroid.faa
examples/input/demo_genecatalogs_counts.all.tsv
examples/input/demo_mgx_metadata.tsv
examples/output/characterization/abundance_annotation/demo_DNA_proteinfamilies.abundance.detail.tsv.gz
examples/output/characterization/abundance_annotation/demo_MSPminer_proteinfamilies.detail.tsv.gz
examples/output/characterization/abundance_annotation/demo_MaAsLin2_proteinfamilies.DA-sig.detail.tsv.gz
examples/output/characterization/abundance_annotation/demo_MaAsLin2_proteinfamilies.DA.detail.tsv.gz
examples/output/characterization/abundance_annotation/demo_proteinfamilies_annotation.taxonomy.tsv.gz
examples/output/characterization/clustering/demo_proteinfamilies.centroid.faa.gz
examples/output/characterization/clustering/demo_proteinfamilies.clstr
examples/output/characterization/domain_motif_annotation/demo_DOMINE_proteinfamilies.detail.tsv.gz
examples/output/characterization/domain_motif_annotation/demo_Denovo_proteinfamilies.signaling.detail.tsv.gz
examples/output/characterization/domain_motif_annotation/demo_Denovo_proteinfamilies.transmembrane.detail.tsv.gz
examples/output/characterization/domain_motif_annotation/demo_InterProScan_proteinfamilies.detail.tsv.gz
examples/output/characterization/finalized/demo_proteinfamilies_annotation.attribute.tsv.gz
examples/output/characterization/finalized/demo_proteinfamilies_annotation.taxonomy.tsv.gz
examples/output/characterization/finalized/demo_proteinfamilies_annotation.tsv.gz
examples/output/characterization/finalized/demo_proteinfamilies_nrm.tsv.gz
examples/output/characterization/global_homology_annotation/demo_UniRef90_proteinfamilies.detail.tsv.gz
examples/output/characterization/global_homology_annotation/demo_proteinfamilies_annotation.uniref90_annotation.tsv.gz
examples/output/preprocess/finalized/demo_genecatalogs.centroid.faa
examples/output/preprocess/finalized/demo_genecatalogs_counts.all.tsv
examples/output/prioritization/demo_supervised_prioritization.rank.selected.table.tsv.gz
examples/output/prioritization/demo_supervised_prioritization.rank.table.tsv.gz
examples/output/prioritization/demo_unsupervised_prioritization.rank.table.tsv.gz
examples/raw_reads/sample1_R1.fastq.gz
examples/raw_reads/sample1_R2.fastq.gz
examples/raw_reads/sample2_R1.fastq.gz
examples/raw_reads/sample2_R2.fastq.gz
metawibele/__init__.py
metawibele/check.py
metawibele/config.py
metawibele/metawibele.py
metawibele/utilities.py
metawibele.egg-info/PKG-INFO
metawibele.egg-info/SOURCES.txt
metawibele.egg-info/dependency_links.txt
metawibele.egg-info/entry_points.txt
metawibele.egg-info/not-zip-safe
metawibele.egg-info/top_level.txt
metawibele/Rscripts/maaslin2_utils.R
metawibele/Rscripts/pcl_utils.R
metawibele/characterize/__init__.py
metawibele/characterize/abundance_annotator.py
metawibele/characterize/ddi_DOMINE_ExpAtlas.py
metawibele/characterize/ddi_DOMINE_SIFTS.py
metawibele/characterize/ddi_DOMINE_ann.py
metawibele/characterize/ddi_DOMINE_protein.py
metawibele/characterize/ddi_DOMINE_protein_family.py
metawibele/characterize/denovo_TM_SP.py
metawibele/characterize/finalize_annotation.py
metawibele/characterize/interproscan_annotator.py
metawibele/characterize/interproscan_pfam_protein_family.py
metawibele/characterize/interproscan_phobius_protein_family.py
metawibele/characterize/interproscan_protein.py
metawibele/characterize/interproscan_protein_family.py
metawibele/characterize/interproscan_signalp_protein_family.py
metawibele/characterize/interproscan_tmhmm_protein_family.py
metawibele/characterize/maaslin2.py
metawibele/characterize/maaslin2_annotator.py
metawibele/characterize/maaslin2_collection.py
metawibele/characterize/maaslin2_summary.py
metawibele/characterize/metadata_format.py
metawibele/characterize/msp_protein_family.py
metawibele/characterize/mspminer_msp.py
metawibele/characterize/mspminer_msp_taxonomy_annotation.py
metawibele/characterize/mspminer_msp_uniref_annotation.py
metawibele/characterize/mspminer_protein.py
metawibele/characterize/mspminer_protein_family.py
metawibele/characterize/mspminer_protein_family_taxonomy.py
metawibele/characterize/pfam2go.py
metawibele/characterize/psortb_annotator.py
metawibele/characterize/psortb_protein.py
metawibele/characterize/psortb_protein_family.py
metawibele/characterize/sum_to_protein_family_abundance.py
metawibele/characterize/summary_all_annotation.py
metawibele/characterize/summary_function_annotation.py
metawibele/characterize/summary_protein_family_uniref_annotation.py
metawibele/characterize/summary_protein_uniref_annotation.py
metawibele/characterize/uniref_annotator.py
metawibele/characterize/uniref_annotator_stat.py
metawibele/characterize/uniref_protein.py
metawibele/characterize/uniref_protein_family.py
metawibele/characterize/utils.py
metawibele/common/__init__.py
metawibele/common/abundance_RPK.py
metawibele/common/abundance_filtering.py
metawibele/common/abundance_normalization.py
metawibele/common/abundance_smoothing.py
metawibele/common/check_install.py
metawibele/common/combine_abundance_annotation.py
metawibele/common/download_config_file.py
metawibele/common/download_database.py
metawibele/common/extract_abundance_feature_subset.py
metawibele/common/extract_abundance_sample_subset.py
metawibele/common/extract_uniprot_pfam.py
metawibele/common/filter_clusters.py
metawibele/common/filter_prevalence.py
metawibele/common/join_family_abundance.py
metawibele/common/prepare_domain_databases.py
metawibele/common/prepare_uniprot_annotation.py
metawibele/common/prepare_uniprot_taxonomy.py
metawibele/common/prepare_uniref_annotation.py
metawibele/common/split_family_abundance.py
metawibele/common/split_fasta_file.py
metawibele/common/transpose.py
metawibele/common/utils.py
metawibele/configs/MSPminer_setting.cfg
metawibele/configs/characterization.cfg
metawibele/configs/metawibele.cfg
metawibele/configs/prioritization.cfg
metawibele/data/domain/32_Uhlen_Lab_colon_rectum.txt.gz
metawibele/data/domain/Encode_sigmoid_colon.txt.gz
metawibele/data/domain/FANTOM5_colon_rectum.txt.gz
metawibele/data/domain/GTEx_sigmoid_transverse_colon.txt.gz
metawibele/data/domain/Human_protein_Atlas_colon_rectum.txt.gz
metawibele/data/domain/Human_proteome_map_colon_rectum.txt.gz
metawibele/data/domain/INTERACTION.txt.gz
metawibele/data/domain/Illumina_Body_Map_colon.txt.gz
metawibele/data/domain/README.txt
metawibele/data/domain/gene_ontology.txt.gz
metawibele/data/domain/pdb_chain_pfam.tsv.gz
metawibele/data/domain/pdb_chain_taxonomy.tsv.gz
metawibele/data/domain/pfam_descriptions.txt.gz
metawibele/data/misc/vignette_function.tsv
metawibele/data/uniref/README.txt
metawibele/data/uniref/map_Rep_TaxID_uniref90.demo.txt.gz
metawibele/data/uniref/map_Rep_Tax_uniref90.demo.txt.gz
metawibele/data/uniref/map_TaxID_uniref90.demo.txt.gz
metawibele/data/uniref/map_Tax_uniref90.demo.txt.gz
metawibele/data/uniref/uniprot_human_pfam.tsv.gz
metawibele/data/uniref/uniprot_taxaID_mammalia.txt.gz
metawibele/data/uniref/uniprot_taxaID_microbiome.txt.gz
metawibele/data/uniref/uniprot_taxonomy.tsv.gz
metawibele/data/uniref/uniref90.demo.fasta.dmnd
metawibele/prioritize/__init__.py
metawibele/prioritize/filter_prioritization.py
metawibele/prioritize/finalize_prioritization.py
metawibele/prioritize/quantify_prioritization.py
metawibele/tasks/__init__.py
metawibele/tasks/characterization.py
metawibele/tasks/prioritization.py
metawibele/tools/__init__.py
metawibele/tools/combine_gene_sequences.py
metawibele/tools/extract_cluster_CD_hit.py
metawibele/tools/extract_complete_ORF_seq.py
metawibele/tools/extract_non_redundance_seq.py
metawibele/tools/extract_protein_coding_genes.py
metawibele/tools/format_contig_sequences.py
metawibele/tools/format_protein_sequences.py
metawibele/tools/gene_abundance.py
metawibele/tools/gene_abundance_indexRef.py
metawibele/tools/gene_catalog_abundance.py
metawibele/tools/preprocessing_tasks.py
metawibele/workflows/characterize.py
metawibele/workflows/preprocess.py
metawibele/workflows/prioritize.py