Analysis protocol

Information about the analysis protocol.

Properties

Alignment softwareanalysis_protocol.alignment_software (string) Name of alignment software used to map FASTQ files to reference genome. For example "Cellranger", "kallisto bustools", "GSNAP" or "STAR".

Alignment software versionanalysis_protocol.alignment_software_version (string) Version of alignment software used to map FASTQ files to reference genome. For example "v2.0.1", "2.4.2a" or "v0.45.2".

Computational methodanalysis_protocol.computational_method (string) A URI to a versioned workflow and versioned execution environment in a GA4GH-compliant repository. For example "SmartSeq2SingleCell" or "10x".

Gene annotation versionanalysis_protocol.gene_annotation_version (string) The Ensembl release version accession number or NCBI RefSeq assembly version used for gene annotation. For example "v110", "GCF_000001405.40" or "GCF_000001635.27".

Intron inclusionanalysis_protocol.intron_inclusion (boolean) Whether introns were included in the alignment process during read counting. For example "Should be one of: yes, or no.".

Data normalization method(s)analysis_protocol.matrix.data_normalization_methods (array from matrix) Method(s) used to normalize data in the matrix

Derivation processanalysis_protocol.matrix.derivation_process (array from matrix) Type of computational tool used in generating the matrix object.

Process type ontology IDanalysis_protocol.type.ontology (string from process_type_ontology) An ontology term identifier in the form prefix:accession. For example "EFO:0009128" or "EFO:0009121".Graph restriction: Subclasses of EFO:0002694 from obo:efo.

Process type ontology labelanalysis_protocol.type.ontology_label (string from process_type_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "enzymatic dissociation" or "blood draw".

Process typeRequiredanalysis_protocol.type.text (string from process_type_ontology) The name of a process type being used. For example "enzymatic dissociation" or "blood draw".

Document filenameanalysis_protocol.protocol_core.document (string from protocol_core) A filename of a PDF document containing the details of the protocol. For example "my_cool_protocol.pdf".

Protocol descriptionanalysis_protocol.protocol_core.protocol_description (string from protocol_core) A general description of the protocol.

Protocol IDRequiredanalysis_protocol.protocol_core.protocol_id (string from protocol_core) A unique ID for the protocol.

Protocol nameanalysis_protocol.protocol_core.protocol_name (string from protocol_core) A short name for the protocol.

protocols.io DOIanalysis_protocol.protocol_core.protocols_io_doi (string from protocol_core) The protocols.io digital object identifier (doi) for the protocol. For example "10.17504/protocols.io.mgjc3un".

Publication DOIanalysis_protocol.protocol_core.publication_doi (string from protocol_core) The publication digital object identifier (doi) for the protocol. For example "10.1101/193219".

Accessionanalysis_protocol.provenance.accession (string from provenance) A unique accession for this entity, provided by the broker.

Document IDRequiredanalysis_protocol.provenance.document_id (string from provenance) Identifier for document.

Schema major versionanalysis_protocol.provenance.schema_major_version (integer from provenance) The major version number of the schema. For example "4" or "10".

Schema minor versionanalysis_protocol.provenance.schema_minor_version (integer from provenance) The minor version number of the schema. For example "6" or "15".

Submission dateRequiredanalysis_protocol.provenance.submission_date (string from provenance) When project was first submitted to database.

Submitter IDanalysis_protocol.provenance.submitter_id (string from provenance) ID of individual who first submitted project.

Update dateanalysis_protocol.provenance.update_date (string from provenance) When project was last updated.

Updater IDanalysis_protocol.provenance.updater_id (string from provenance) ID of individual who last updated project.