maayanlab_bioinformatics package

Subpackages

• maayanlab_bioinformatics.api package
  • Submodules
  • maayanlab_bioinformatics.api.enrichr module
    • EnrichrUserList
      • EnrichrUserList.description
      • EnrichrUserList.from_url()
      • EnrichrUserList.genes
      • EnrichrUserList.link
      • EnrichrUserList.shortId
      • EnrichrUserList.userListId
    • enrichr_get_top_results()
    • enrichr_link_from_genes()
    • enrichr_term_genes()
  • maayanlab_bioinformatics.api.speedrichr module
    • speedenrich()
  • Module contents
• maayanlab_bioinformatics.clustering package
  • Submodules
  • maayanlab_bioinformatics.clustering.silhouette_analysis module
    • silhouette_analysis()
  • Module contents
• maayanlab_bioinformatics.dge package
  • Submodules
  • maayanlab_bioinformatics.dge.characteristic_direction module
    • characteristic_direction()
    • up_down_from_characteristic_direction()
  • maayanlab_bioinformatics.dge.deseq2 module
    • deseq2_differential_expression()
  • maayanlab_bioinformatics.dge.limma_voom module
    • limma_voom_differential_expression()
    • limma_voom_differential_expression_design()
    • make_design_matrix()
    • up_down_from_limma_voom()
  • maayanlab_bioinformatics.dge.logfc module
    • logfc_differential_expression()
  • maayanlab_bioinformatics.dge.ttest module
    • ttest_differential_expression()
  • Module contents
• maayanlab_bioinformatics.enrichment package
  • Submodules
  • maayanlab_bioinformatics.enrichment.crisp module
    • FisherOverlap
      • FisherOverlap.n_overlap
      • FisherOverlap.odds_ratio
      • FisherOverlap.overlap
      • FisherOverlap.pvalue
    • enrich_crisp()
    • fisher_overlap()
    • safe_odds_ratio()
  • maayanlab_bioinformatics.enrichment.gsea2003 module
    • GSEA2003()
  • maayanlab_bioinformatics.enrichment.gsea2005 module
    • GSEA2005()
  • Module contents
• maayanlab_bioinformatics.harmonization package
  • Submodules
  • maayanlab_bioinformatics.harmonization.homologs module
    • human_expression_to_mouse()
    • mouse_expression_to_human()
    • mouse_human_homologs()
  • maayanlab_bioinformatics.harmonization.id_mapper module
    • IDMapper
      • IDMapper.conflicts_summary()
      • IDMapper.find()
      • IDMapper.get()
      • IDMapper.get_id()
      • IDMapper.summary()
      • IDMapper.top_conflicts()
      • IDMapper.update()
  • maayanlab_bioinformatics.harmonization.ncbi_genes module
    • ncbi_genes_fetch()
    • ncbi_genes_lookup()
  • maayanlab_bioinformatics.harmonization.transcripts module
    • transcripts_to_genes()
  • Module contents
• maayanlab_bioinformatics.normalization package
  • Submodules
  • maayanlab_bioinformatics.normalization.cpm module
    • cpm_normalize()
    • cpm_normalize_np()
    • cpm_normalize_pd()
  • maayanlab_bioinformatics.normalization.filter module
    • filter_by_expr()
    • filter_by_var()
  • maayanlab_bioinformatics.normalization.log module
    • log10_normalize()
    • log10_normalize_np()
    • log10_normalize_pd()
    • log10_normalize_pds()
    • log2_normalize()
    • log2_normalize_np()
    • log2_normalize_pd()
    • log2_normalize_pds()
  • maayanlab_bioinformatics.normalization.quantile module
  • maayanlab_bioinformatics.normalization.quantile_legacy module
    • quantile_normalize()
    • quantile_normalize_h5()
    • quantile_normalize_np()
    • quantile_normalize_pd()
  • maayanlab_bioinformatics.normalization.zscore module
    • zscore_normalize()
    • zscore_normalize_np()
    • zscore_normalize_pd()
    • zscore_normalize_pds()
  • Module contents
• maayanlab_bioinformatics.parse package
  • Submodules
  • maayanlab_bioinformatics.parse.gmt module
    • gmt_read_dict()
    • gmt_read_iter()
    • gmt_read_pd()
    • gmt_write_dict()
    • gmt_write_pd()
    • parse_gene_unweighted()
    • parse_gene_weight()
  • maayanlab_bioinformatics.parse.suerat module
    • suerat_load()
    • suerat_load_multiple()
  • Module contents
• maayanlab_bioinformatics.plotting package
  • Submodules
  • maayanlab_bioinformatics.plotting.bridge module
    • bridge_plot()
  • maayanlab_bioinformatics.plotting.clustergrammer module
    • display_clustergrammer()
  • maayanlab_bioinformatics.plotting.upset module
    • upset_from_dict_of_sets()
  • Module contents
• maayanlab_bioinformatics.utils package
  • Submodules
  • maayanlab_bioinformatics.utils.chunked module
    • chunk_applymap()
    • chunk_infer()
    • chunk_slices()
    • tqdm()
  • maayanlab_bioinformatics.utils.describe module
    • np_describe()
  • maayanlab_bioinformatics.utils.fetch_save_read module
    • fetch_save_read()
  • maayanlab_bioinformatics.utils.merge module
    • merge()
  • maayanlab_bioinformatics.utils.sparse module
    • sp_hdf_dump()
    • sp_hdf_load()
    • sp_nanpercentile()
    • sp_std()
  • Module contents

Module contents

A collection of useful functions for bioinformatics data analysis.

This library contains many functions and methods I use again and again in different analyses including:

• api: enrichr, l1000fwd, …

• clustering: silhouette analysis, …

• dge: various differential gene expression techniques including chdir, lima_voom, ..

• harmonization: transcript to gene conversions, …

• normalization: log, cpm, zscore, filterByExpr, quantile, …

• parse: gmt, suerat ready files, …

• utils: fetch_save_read, merge, …