Index

B

bridge_plot() (in module maayanlab_bioinformatics.plotting.bridge)

C

characteristic_direction() (in module maayanlab_bioinformatics.dge.characteristic_direction) chunk_applymap() (in module maayanlab_bioinformatics.utils.chunked) chunk_infer() (in module maayanlab_bioinformatics.utils.chunked) chunk_slices() (in module maayanlab_bioinformatics.utils.chunked)

conflicts_summary() (maayanlab_bioinformatics.harmonization.id_mapper.IDMapper method) cpm_normalize() (in module maayanlab_bioinformatics.normalization.cpm) cpm_normalize_np() (in module maayanlab_bioinformatics.normalization.cpm) cpm_normalize_pd() (in module maayanlab_bioinformatics.normalization.cpm)

D

description (maayanlab_bioinformatics.api.enrichr.EnrichrUserList property)

deseq2_differential_expression() (in module maayanlab_bioinformatics.dge.deseq2) display_clustergrammer() (in module maayanlab_bioinformatics.plotting.clustergrammer)

E

enrich_crisp() (in module maayanlab_bioinformatics.enrichment.crisp) enrichr_get_top_results() (in module maayanlab_bioinformatics.api.enrichr)

enrichr_link_from_genes() (in module maayanlab_bioinformatics.api.enrichr) enrichr_term_genes() (in module maayanlab_bioinformatics.api.enrichr) EnrichrUserList (class in maayanlab_bioinformatics.api.enrichr)

F

fetch_save_read() (in module maayanlab_bioinformatics.utils.fetch_save_read) filter_by_expr() (in module maayanlab_bioinformatics.normalization.filter) filter_by_var() (in module maayanlab_bioinformatics.normalization.filter)

find() (maayanlab_bioinformatics.harmonization.id_mapper.IDMapper method) fisher_overlap() (in module maayanlab_bioinformatics.enrichment.crisp) FisherOverlap (class in maayanlab_bioinformatics.enrichment.crisp) from_url() (maayanlab_bioinformatics.api.enrichr.EnrichrUserList static method)

G

genes (maayanlab_bioinformatics.api.enrichr.EnrichrUserList property) get() (maayanlab_bioinformatics.harmonization.id_mapper.IDMapper method) get_id() (maayanlab_bioinformatics.harmonization.id_mapper.IDMapper method) gmt_read_dict() (in module maayanlab_bioinformatics.parse.gmt) gmt_read_iter() (in module maayanlab_bioinformatics.parse.gmt)

gmt_read_pd() (in module maayanlab_bioinformatics.parse.gmt) gmt_write_dict() (in module maayanlab_bioinformatics.parse.gmt) gmt_write_pd() (in module maayanlab_bioinformatics.parse.gmt) GSEA2003() (in module maayanlab_bioinformatics.enrichment.gsea2003) GSEA2005() (in module maayanlab_bioinformatics.enrichment.gsea2005)

H

human_expression_to_mouse() (in module maayanlab_bioinformatics.harmonization.homologs)

I

IDMapper (class in maayanlab_bioinformatics.harmonization.id_mapper)

L

limma_voom_differential_expression() (in module maayanlab_bioinformatics.dge.limma_voom) limma_voom_differential_expression_design() (in module maayanlab_bioinformatics.dge.limma_voom) link (maayanlab_bioinformatics.api.enrichr.EnrichrUserList property) log10_normalize() (in module maayanlab_bioinformatics.normalization.log) log10_normalize_np() (in module maayanlab_bioinformatics.normalization.log) log10_normalize_pd() (in module maayanlab_bioinformatics.normalization.log)

log10_normalize_pds() (in module maayanlab_bioinformatics.normalization.log) log2_normalize() (in module maayanlab_bioinformatics.normalization.log) log2_normalize_np() (in module maayanlab_bioinformatics.normalization.log) log2_normalize_pd() (in module maayanlab_bioinformatics.normalization.log) log2_normalize_pds() (in module maayanlab_bioinformatics.normalization.log) logfc_differential_expression() (in module maayanlab_bioinformatics.dge.logfc)

M

maayanlab_bioinformatics module maayanlab_bioinformatics.api module maayanlab_bioinformatics.api.enrichr module maayanlab_bioinformatics.api.speedrichr module maayanlab_bioinformatics.clustering module maayanlab_bioinformatics.clustering.silhouette_analysis module maayanlab_bioinformatics.dge module maayanlab_bioinformatics.dge.characteristic_direction module maayanlab_bioinformatics.dge.deseq2 module maayanlab_bioinformatics.dge.limma_voom module maayanlab_bioinformatics.dge.logfc module maayanlab_bioinformatics.dge.ttest module maayanlab_bioinformatics.enrichment module maayanlab_bioinformatics.enrichment.crisp module maayanlab_bioinformatics.enrichment.gsea2003 module maayanlab_bioinformatics.enrichment.gsea2005 module maayanlab_bioinformatics.harmonization module maayanlab_bioinformatics.harmonization.homologs module maayanlab_bioinformatics.harmonization.id_mapper module maayanlab_bioinformatics.harmonization.ncbi_genes module maayanlab_bioinformatics.harmonization.transcripts module maayanlab_bioinformatics.normalization module maayanlab_bioinformatics.normalization.cpm module maayanlab_bioinformatics.normalization.filter module maayanlab_bioinformatics.normalization.log module maayanlab_bioinformatics.normalization.quantile module maayanlab_bioinformatics.normalization.quantile_legacy module maayanlab_bioinformatics.normalization.zscore module maayanlab_bioinformatics.parse module maayanlab_bioinformatics.parse.gmt module maayanlab_bioinformatics.parse.suerat module maayanlab_bioinformatics.plotting module

maayanlab_bioinformatics.plotting.bridge module maayanlab_bioinformatics.plotting.clustergrammer module maayanlab_bioinformatics.plotting.upset module maayanlab_bioinformatics.utils module maayanlab_bioinformatics.utils.chunked module maayanlab_bioinformatics.utils.describe module maayanlab_bioinformatics.utils.fetch_save_read module maayanlab_bioinformatics.utils.merge module maayanlab_bioinformatics.utils.sparse module make_design_matrix() (in module maayanlab_bioinformatics.dge.limma_voom) merge() (in module maayanlab_bioinformatics.utils.merge) module maayanlab_bioinformatics maayanlab_bioinformatics.api maayanlab_bioinformatics.api.enrichr maayanlab_bioinformatics.api.speedrichr maayanlab_bioinformatics.clustering maayanlab_bioinformatics.clustering.silhouette_analysis maayanlab_bioinformatics.dge maayanlab_bioinformatics.dge.characteristic_direction maayanlab_bioinformatics.dge.deseq2 maayanlab_bioinformatics.dge.limma_voom maayanlab_bioinformatics.dge.logfc maayanlab_bioinformatics.dge.ttest maayanlab_bioinformatics.enrichment maayanlab_bioinformatics.enrichment.crisp maayanlab_bioinformatics.enrichment.gsea2003 maayanlab_bioinformatics.enrichment.gsea2005 maayanlab_bioinformatics.harmonization maayanlab_bioinformatics.harmonization.homologs maayanlab_bioinformatics.harmonization.id_mapper maayanlab_bioinformatics.harmonization.ncbi_genes maayanlab_bioinformatics.harmonization.transcripts maayanlab_bioinformatics.normalization maayanlab_bioinformatics.normalization.cpm maayanlab_bioinformatics.normalization.filter maayanlab_bioinformatics.normalization.log maayanlab_bioinformatics.normalization.quantile maayanlab_bioinformatics.normalization.quantile_legacy maayanlab_bioinformatics.normalization.zscore maayanlab_bioinformatics.parse maayanlab_bioinformatics.parse.gmt maayanlab_bioinformatics.parse.suerat maayanlab_bioinformatics.plotting maayanlab_bioinformatics.plotting.bridge maayanlab_bioinformatics.plotting.clustergrammer maayanlab_bioinformatics.plotting.upset maayanlab_bioinformatics.utils maayanlab_bioinformatics.utils.chunked maayanlab_bioinformatics.utils.describe maayanlab_bioinformatics.utils.fetch_save_read maayanlab_bioinformatics.utils.merge maayanlab_bioinformatics.utils.sparse mouse_expression_to_human() (in module maayanlab_bioinformatics.harmonization.homologs) mouse_human_homologs() (in module maayanlab_bioinformatics.harmonization.homologs)

N

n_overlap (maayanlab_bioinformatics.enrichment.crisp.FisherOverlap attribute) ncbi_genes_fetch() (in module maayanlab_bioinformatics.harmonization.ncbi_genes)

ncbi_genes_lookup() (in module maayanlab_bioinformatics.harmonization.ncbi_genes) np_describe() (in module maayanlab_bioinformatics.utils.describe)

O

odds_ratio (maayanlab_bioinformatics.enrichment.crisp.FisherOverlap attribute)

overlap (maayanlab_bioinformatics.enrichment.crisp.FisherOverlap attribute)

P

parse_gene_unweighted() (in module maayanlab_bioinformatics.parse.gmt)

parse_gene_weight() (in module maayanlab_bioinformatics.parse.gmt) pvalue (maayanlab_bioinformatics.enrichment.crisp.FisherOverlap attribute)

Q

quantile_normalize() (in module maayanlab_bioinformatics.normalization.quantile_legacy) quantile_normalize_h5() (in module maayanlab_bioinformatics.normalization.quantile_legacy)

quantile_normalize_np() (in module maayanlab_bioinformatics.normalization.quantile_legacy) quantile_normalize_pd() (in module maayanlab_bioinformatics.normalization.quantile_legacy)

S

safe_odds_ratio() (in module maayanlab_bioinformatics.enrichment.crisp) shortId (maayanlab_bioinformatics.api.enrichr.EnrichrUserList property) silhouette_analysis() (in module maayanlab_bioinformatics.clustering.silhouette_analysis) sp_hdf_dump() (in module maayanlab_bioinformatics.utils.sparse) sp_hdf_load() (in module maayanlab_bioinformatics.utils.sparse)

sp_nanpercentile() (in module maayanlab_bioinformatics.utils.sparse) sp_std() (in module maayanlab_bioinformatics.utils.sparse) speedenrich() (in module maayanlab_bioinformatics.api.speedrichr) suerat_load() (in module maayanlab_bioinformatics.parse.suerat) suerat_load_multiple() (in module maayanlab_bioinformatics.parse.suerat) summary() (maayanlab_bioinformatics.harmonization.id_mapper.IDMapper method)

T

top_conflicts() (maayanlab_bioinformatics.harmonization.id_mapper.IDMapper method) tqdm() (in module maayanlab_bioinformatics.utils.chunked)

transcripts_to_genes() (in module maayanlab_bioinformatics.harmonization.transcripts) ttest_differential_expression() (in module maayanlab_bioinformatics.dge.ttest)

U

up_down_from_characteristic_direction() (in module maayanlab_bioinformatics.dge.characteristic_direction) up_down_from_limma_voom() (in module maayanlab_bioinformatics.dge.limma_voom)

update() (maayanlab_bioinformatics.harmonization.id_mapper.IDMapper method) upset_from_dict_of_sets() (in module maayanlab_bioinformatics.plotting.upset) userListId (maayanlab_bioinformatics.api.enrichr.EnrichrUserList property)

Z

zscore_normalize() (in module maayanlab_bioinformatics.normalization.zscore) zscore_normalize_np() (in module maayanlab_bioinformatics.normalization.zscore)

zscore_normalize_pd() (in module maayanlab_bioinformatics.normalization.zscore) zscore_normalize_pds() (in module maayanlab_bioinformatics.normalization.zscore)