.gitignore
.pre-commit-config.yaml
.readthedocs.yaml
CONTRIBUTING.md
LICENSE
MANIFEST.in
README.md
pyproject.toml
.github/scripts/ci_python_versions.py
.github/workflows/coverage.yaml
.github/workflows/release.yaml
.github/workflows/test_ftp_loader.yaml
.github/workflows/test_macos_arm64.yaml
.github/workflows/test_ubuntu_x64.yaml
data/README.md
data/annotations/custom_GCF_000001405.40.chr16.vcf
data/annotations/custom_GCF_000001405.40_GRCh38.p14_genomic_chr16.fna
data/annotations/custom_GCF_000001405.40_GRCh38.p14_genomic_chr16.fna.fai
data/annotations/custom_GCF_000001405.40_GRCh38.p14_genomic_chr16.gtf
data/configs/cycle_hcr_probe_designer.yaml
data/configs/genomic_region_generator_custom.yaml
data/configs/genomic_region_generator_ensemble.yaml
data/configs/genomic_region_generator_ncbi.yaml
data/configs/hcr_probe_designer.yaml
data/configs/merfish_probe_designer.yaml
data/configs/oligo_seq_probe_designer.yaml
data/configs/scrinshot_probe_designer.yaml
data/configs/seqfish_plus_probe_designer.yaml
data/functional_oligos/cycle_hcr_codebook.tsv
data/functional_oligos/cycle_hcr_readout_probes_no_codebook.tsv
data/functional_oligos/cycle_hcr_readout_probes_with_codebook.tsv
data/functional_oligos/hcr_codebook.tsv
data/functional_oligos/hcr_initiators.tsv
data/genes/custom_10.txt
data/genes/custom_100.txt
data/genes/custom_200.txt
data/genes/custom_3.txt
data/genomic_regions/cds_annotation_source-NCBI_species-Homo_sapiens_annotation_release-110_genome_assemly-GRCh38.fna
data/genomic_regions/exon_annotation_source-NCBI_species-Homo_sapiens_annotation_release-110_genome_assemly-GRCh38.fna
data/genomic_regions/exon_exon_junction_annotation_source-NCBI_species-Homo_sapiens_annotation_release-110_genome_assemly-GRCh38.fna
data/genomic_regions/gene_annotation_source-NCBI_species-Homo_sapiens_annotation_release-110_genome_assemly-GRCh38.fna
data/genomic_regions/intron_annotation_source-NCBI_species-Homo_sapiens_annotation_release-110_genome_assemly-GRCh38.fna
data/genomic_regions/utr_annotation_source-NCBI_species-Homo_sapiens_annotation_release-110_genome_assemly-GRCh38.fna
oligo_designer_toolsuite/__init__.py
oligo_designer_toolsuite/_constants.py
oligo_designer_toolsuite/_exceptions.py
oligo_designer_toolsuite/_version.py
oligo_designer_toolsuite.egg-info/PKG-INFO
oligo_designer_toolsuite.egg-info/SOURCES.txt
oligo_designer_toolsuite.egg-info/dependency_links.txt
oligo_designer_toolsuite.egg-info/entry_points.txt
oligo_designer_toolsuite.egg-info/requires.txt
oligo_designer_toolsuite.egg-info/top_level.txt
oligo_designer_toolsuite/database/__init__.py
oligo_designer_toolsuite/database/_oligo_database.py
oligo_designer_toolsuite/database/_reference_database.py
oligo_designer_toolsuite/oligo_efficiency_filter/__init__.py
oligo_designer_toolsuite/oligo_efficiency_filter/_oligo_scoring.py
oligo_designer_toolsuite/oligo_efficiency_filter/_scorer_base.py
oligo_designer_toolsuite/oligo_efficiency_filter/_scorer_region_property.py
oligo_designer_toolsuite/oligo_efficiency_filter/_scorer_sequence_property.py
oligo_designer_toolsuite/oligo_efficiency_filter/_scorer_set_property.py
oligo_designer_toolsuite/oligo_efficiency_filter/_set_scoring.py
oligo_designer_toolsuite/oligo_property_calculator/__init__.py
oligo_designer_toolsuite/oligo_property_calculator/_property_base.py
oligo_designer_toolsuite/oligo_property_calculator/_property_calculator.py
oligo_designer_toolsuite/oligo_property_calculator/_property_functions.py
oligo_designer_toolsuite/oligo_property_calculator/_property_region.py
oligo_designer_toolsuite/oligo_property_calculator/_property_sequence.py
oligo_designer_toolsuite/oligo_property_filter/__init__.py
oligo_designer_toolsuite/oligo_property_filter/_filter_base.py
oligo_designer_toolsuite/oligo_property_filter/_filter_experiment_specific.py
oligo_designer_toolsuite/oligo_property_filter/_filter_experiment_unspecific.py
oligo_designer_toolsuite/oligo_property_filter/_property_filter.py
oligo_designer_toolsuite/oligo_selection/__init__.py
oligo_designer_toolsuite/oligo_selection/_oligo_selection_base.py
oligo_designer_toolsuite/oligo_selection/_oligo_selection_homogeneous_properties.py
oligo_designer_toolsuite/oligo_selection/_oligo_selection_independent_sets.py
oligo_designer_toolsuite/oligo_specificity_filter/__init__.py
oligo_designer_toolsuite/oligo_specificity_filter/_filter_base.py
oligo_designer_toolsuite/oligo_specificity_filter/_filter_blastn.py
oligo_designer_toolsuite/oligo_specificity_filter/_filter_bowtie.py
oligo_designer_toolsuite/oligo_specificity_filter/_filter_cross_hybridization.py
oligo_designer_toolsuite/oligo_specificity_filter/_filter_exact_matches.py
oligo_designer_toolsuite/oligo_specificity_filter/_filter_hybridization_probability.py
oligo_designer_toolsuite/oligo_specificity_filter/_filter_variants.py
oligo_designer_toolsuite/oligo_specificity_filter/_policies.py
oligo_designer_toolsuite/oligo_specificity_filter/_specificity_filter.py
oligo_designer_toolsuite/pipelines/__init__.py
oligo_designer_toolsuite/pipelines/_cycle_hcr_probe_designer.py
oligo_designer_toolsuite/pipelines/_genomic_region_generator.py
oligo_designer_toolsuite/pipelines/_hcr_probe_designer.py
oligo_designer_toolsuite/pipelines/_merfish_probe_designer.py
oligo_designer_toolsuite/pipelines/_oligo_seq_probe_designer.py
oligo_designer_toolsuite/pipelines/_scrinshot_probe_designer.py
oligo_designer_toolsuite/pipelines/_seqfish_plus_probe_designer.py
oligo_designer_toolsuite/pipelines/_utils.py
oligo_designer_toolsuite/sequence_generator/__init__.py
oligo_designer_toolsuite/sequence_generator/_ftp_loader.py
oligo_designer_toolsuite/sequence_generator/_genomic_region_generator.py
oligo_designer_toolsuite/sequence_generator/_oligo_sequence_generator.py
oligo_designer_toolsuite/utils/__init__.py
oligo_designer_toolsuite/utils/_checkers_and_helpers.py
oligo_designer_toolsuite/utils/_database_processor.py
oligo_designer_toolsuite/utils/_sequence_parser.py
oligo_designer_toolsuite/utils/_sequence_processor.py