🚀 Getting Started
📖 User Guide
sirnaforge zfn
top_candidates
📚 Reference
ReferenceChoice
ReferenceSelection
ReferencePolicyResolver
ReferenceState
WorkflowInputSpec
render_reference_selection_label()
patched_init()
TranscriptLike
TranscriptLike.transcript_type
TranscriptLike.is_canonical
TranscriptLike.__init__()
filter_transcripts()
extract_canonical_transcripts()
search()
workflow()
offtarget()
zfn()
design()
validate()
version()
config()
cache()
SequencesShowError
sequences_show()
sequences_annotate()
internal_zfn_make_shards()
internal_zfn_build_search_index()
internal_zfn_search_shard()
internal_zfn_aggregate_shards()
SiRNADesigner
mirna_max_biogenesis_bonus()
apply_mirna_biogenesis_bonus()
MiRNADesigner
ThermodynamicCalculator
BwaAnalyzer
OffTargetAnalysisManager
MiRNASeedBackend
create_temp_fasta()
validate_and_write_sequences()
build_bwa_index()
validate_sirna_sequences()
parse_fasta_file()
write_fasta_file()
check_tool_availability()
validate_index_files()
mirna_seed_hit_identity()
normalize_mirna_seed_hit()
run_bwa_alignment_analysis()
aggregate_offtarget_results()
scan_mirna_seed_matches()
run_mirna_seed_analysis()
aggregate_mirna_results()
emit_zfn_experimental_warning()
reset_zfn_experimental_warning()
ZFNDesigner
build_zfn_search_index()
resolve_target_contigs()
build_zfn_shard_specs()
ExhaustiveZFNOffTargetSearcher
rank_sites()
GTFZFNAnnotationProvider
ZFNOffTargetSearcher
ZFNAnnotationProvider
ZFNShardRow
make_zfn_shard_manifest()
run_zfn_shard_search()
aggregate_zfn_shard_results()
CCR5S10VisibleRow
CCR5S11HomologyRow
MatchType
load_ccr5_s10_visible_rows()
load_ccr5_s11_homology_rows()
parse_hg19_coordinate()
parse_match_type()
FilterCriteria
OffTargetFilterCriteria
ScoringWeights
DesignMode
MiRNADesignConfig
DesignParameters
SequenceType
SiRNACandidate
build_candidate_row()
DesignResult
ConfirmationStatus
SourceType
Provenance
ChemicalModification
StrandRole
StrandMetadata
SequenceRecord
AlignmentStrand
AnalysisMode
MiRNADatabase
BaseAlignmentHit
OffTargetHit
MiRNAHit
BaseSummary
AnalysisSummary
MiRNASummary
BaseAggregatedSummary
AggregatedOffTargetSummary
AggregatedMiRNASummary
Strand
DimerMode
ZFNAlgorithm
MatchOrientation
IUPACMode
ZFNSearchBackend
ZFNHalfSiteConstraints
ZFNSpacerConstraints
ZFNOffTargetFilterCriteria
ZFNScoringWeights
ZFNMutationType
ZFNSubfingerMutationConstraint
ZFNDefaultSubfingerMutationConstraint
ZFNOverallMutationConstraint
ZFNMutationConstraints
ZFNShardingConfig
ZFNDesignParameters
ZFNSearchContract
GenomicAnnotationConfig
ZFNOffTargetSite
ZFNCandidate
ZFNDesignResult
Interval
TranscriptAnnotation
TranscriptAnnotationBundle
VariantMode
VariantSource
ClinVarSignificance
EnsemblMapping
EnsemblPopulationFrequency
EnsemblVariationResponse
ClinVarVariationResponse
VariantRecord
VariantQueryType
VariantQuery
SchemaConfig
SiRNACandidateSchema
ORFValidationSchema
OffTargetHitsSchema
MiRNAAlignmentSchema
GenomeAlignmentSchema
DatabaseError
DatabaseAccessError
GeneNotFoundError
DatabaseType
GeneInfo
TranscriptInfo
AbstractDatabaseClient
AbstractTranscriptAnnotationClient
EnsemblClient
RefSeqClient
GencodeClient
SequenceUtils
FastaUtils
get_database_display_name()
AnnotationSource
AnnotationManager
GeneSearchResult
GeneSearcher
search_gene_sync()
search_gene_with_fallback_sync()
search_multiple_databases_sync()
ORFInfo
SequenceAnalysis
ORFAnalyzer
create_orf_analyzer()
analyze_multiple_transcript_orfs()
GenomeManager
ReferenceSource
CacheMetadata
ReferenceManager
TranscriptomeSource
TranscriptomeManager
TranscriptFilter
get_filter_spec()
EnsemblTranscriptModelClient
VepConsequenceClient
MiRNASource
MiRNADatabaseManager
main()
normalize_species_name()
VariantResolver
resolve_variant_sync()
VariantParquetCache
generate_contexts_for_variant()
check_candidate_overlaps_variant()
annotate_candidate_with_variant()
apply_variant_to_sequence()
get_variant_position_in_transcript()
build_bwa_index_cli()
aggregate_results_cli()
aggregate_mirna_results_cli()
EnvironmentInfo
NextflowConfig
NextflowRunner
NextflowExecutionError
get_resource_path()
get_test_data_path()
validate_test_data()
ResourceManager
WorkflowConfig
WorkflowConfig.__init__()
ZFNWorkflowConfig
ZFNWorkflowConfig.__init__()
SiRNAWorkflow
SiRNAWorkflow.__init__()
SiRNAWorkflow.run_complete_workflow()
SiRNAWorkflow.step1_retrieve_transcripts()
SiRNAWorkflow.resolve_variants_step()
SiRNAWorkflow.step2_validate_orfs()
SiRNAWorkflow.step3_design_sirnas()
SiRNAWorkflow.step6_generate_reports()
SiRNAWorkflow.step5_offtarget_analysis()
SiRNAWorkflow.run_nextflow_offtarget_analysis()
apply_zfn_runtime_overrides()
run_sirna_workflow()
run_offtarget_only_workflow()
VariantWorkflowConfig
resolve_workflow_variants()
normalize_variant_mode()
parse_clinvar_filter_string()
ValidationLevel
ValidationStage
ValidationConfig
ValidationPresets
ValidationReport
ValidationMiddleware
ValidationResult
ValidationUtils
configure_logging()
get_logger()
resolve_cache_subdir()
stable_cache_key()
LEGACY_PRODUCER_VERSION
PRODUCER_VERSION_FIELD
current_producer_version()
normalize_producer_version()
is_producer_version_current()
log_discarded_artifact()
STAMP_FULL_DIGEST_MAX_BYTES
STAMP_SAMPLE_BYTES
artifact_stamp_path()
fingerprint_outputs()
fingerprint_inputs()
write_artifact_stamp()
read_artifact_stamp()
discard_artifact_stamp()
is_artifact_stamp_current()
parse_csv()
parse_required_csv()
parse_optional_csv()
extract_override_species_from_offtarget_indices()
SpeciesResolution
resolve_species_inputs()
inject_dirty_controls()
load_fasta_sequences()
load_fasta_contig_lengths()
apply_standard_2ome_pattern()
apply_minimal_terminal_pattern()
apply_maximal_stability_pattern()
get_modification_pattern()
apply_modifications_to_candidate()
get_modification_summary()
InputSource
resolve_input_source()
bucket_species()
human_vs_other_totals()
is_human_species()
normalize_species_label()
field_validator_typed()
field_serializer_typed()
check_types_typed()
model_validator_typed()
command_decorator_typed()
CacheStats
ClearResult
CacheComponent
UnifiedCacheManager
parse_chem_mods()
parse_provenance()
parse_header()
load_metadata()
merge_metadata_into_fasta()
save_metadata_json()
sirnaforge.core.hit_classification.HitClass
🔧 Developer
cli.py
sirnaforge.config
workflow.py
core/
models/
data/
validation/
pipeline/
tests/unit/
tests/integration/
tests/pipeline/
src/sirnaforge/models/modifications.py
src/sirnaforge/modifications.py
pyahocorasick
fm_index
exhaustive_python