Connectivity API


You can use this API to connect your third-party application to PIPA data and results.

Genomes sequence and annotation


  • list: returns list of available genomes
  • get_seq: get genomic sequence
    • genomes_id: id of genome
    • chr: chromosome id
    • start: starting position of sequence
    • stop: ending position
    • rev_comp: 0 = do not reverse complement; 1 = reverse complement
  • genes: list of genes
    • genomes_id: id of genome
    • search: string search across gene names and ids
    • mapability: 1/0 (default 0); add mapability information to each gene
    • json: 1/0 (default 0); determines if returned result is text tab delimited or JSON encoded

Mappings (alignments) of reads


  • list: list of available mappings
    • pipa_username: PIPA username, public if not specified
    • pipa_password: PIPA password, public if not specified
  • coverage: coverage of given mapping
    • pipa_username: PIPA username, public if not specified
    • pipa_password: PIPA password, public if not specified
    • id: data and mappings id (e.g. D1_M1)
    • chr: name of chromosome
    • strand: forward/reverse, if omitted, data for both strands is returned
    • start: start position (1-indexed), if omitted, set to 1
    • stop: stop position (1-indexed, included), if omitted, set to end of chromosome
    • position: 5prime (default, counts 1 at each read 5′), span (counts 1 across entire read), span_coverage (place 1 on covered positions)
  • mapping_stats: statistics of give mapping
    • pipa_username: PIPA username, public if not specified
    • pipa_password: PIPA password, public if not specified
    • id: id of mapping
    • json: 1/0 (default 0); determines if returned result is text tab delimited or JSON encoded

Results (gene expression, ChIP-seq)


  • results_templates: list of available result templates
  • results: list of available results
    • pipa_username: PIPA username, public if not specified
    • pipa_password: PIPA password, public if not specified
    • results_templates_id: id from result templates list (e.g. R1)
  • download: list of available results
    • pipa_username: PIPA username, public if not specified
    • pipa_password: PIPA password, public if not specified
    • ids: list of unique_ids from results list (e.g. D1_M1_R1, D2_M1_R1, D3_M1_R1)

Gene expression profiles


  • profiles: gene expression profiles
    • pipa_username: PIPA username, public if not specified
    • pipa_password: PIPA password, public if not specified
    • search: string search profile name
    • json: 1/0 (default 0); determines if returned result is text tab delimited or JSON encoded
  • profiles_expression: expression of genes in selected profile
    • pipa_username: PIPA username, public if not specified
    • pipa_password: PIPA password, public if not specified
    • profiles_id: id of profile
    • json: 1/0 (default 0); determines if returned result is text tab delimited or JSON encoded