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sjandClaude Opus 5 90033214b4 wip: qa7920 sidecar + rag stream timeout 
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
2026-08-21 11:04:28 +08:00
..
_backup_unused_scripts
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
__init__.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
.run_interspecies_synteny.py.swp
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
autofill_common.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
resolve_scope.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
rnaseq_env.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_annotation.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_combo_panel_test.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_combo.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_config_autofill.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_domain.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_expression.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_fetch_expression.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_gene_family_report.py
feat: add gene family result reports
2026-08-09 04:32:28 +08:00
run_genome_prepare.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_genome_prepare.py.bak_family_allpep_20260504_193257
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_gwas_covariate.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_gwas_emmax_plot.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_gwas_emmax.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_gwas_kinship.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_gwas_plot.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_gwas_tassel_glm.py
Initial commit: PlantAI-dev
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run_gwas_tassel_mlm.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_gwas_tassel.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_gwas_trait.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_identify_refine.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_identify.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_identify.py.bak_family_allpep_20260504_193257
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_interspecies_synteny.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_interspecies_synteny.py.bak_blast_engine
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_interspecies_synteny.py.bak_family_allpep_20260504_193257
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_interspecies_synteny.py.bak_highlight_local
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_interspecies_synteny.py.bak_pairwise_20260504_165043
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_interspecies_synteny.py.bak_species_select
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_kaks_v2.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_karyotype.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_motif.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_msa_region_plot.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_ncbi_fetch_sequences.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_ortholog.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_pep_legacy_20260603.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_pep_v2_preview_20260603.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_pep.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_phylogeny.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_pop_ld_decay.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_pop_pca.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_pop_phylogeny.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_pop_snp_density.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_pop_structure.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_ppi_v2.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_ppi.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_prepare_substep.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_promoter_plot_revise.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_promoter.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_reference_classification.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_rnaseq_align.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_rnaseq_candidate_family.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_rnaseq_de.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_rnaseq_enrich_v2.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_rnaseq_enrich.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_rnaseq_family_score.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_rnaseq_fgsea.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_rnaseq_qc.py
wip: qa7920 sidecar + rag stream timeout
2026-08-21 11:04:28 +08:00
run_rnaseq_qc.py.bak.20260430_050459
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_rnaseq_quant.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_rnaseq_report.py
feat:sync-report-workflows-and-migration-runtime
2026-08-10 11:40:20 +08:00
run_rnaseq_sample_qc.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_rnaseq_wgcna.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_samples_autofill.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_sequence_extract_by_id.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_structure.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_structure.py.bak_20260719_target_only
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_subfamily_confirm.py
Add memory directory
2026-08-07 09:39:30 +08:00
run_summary.py
feat: deepseek summary agent + clean old memory logs + merge prep
2026-08-09 09:04:27 +08:00
run_synteny.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_tfbs.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_tree_plot.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_wgs_align.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_wgs_bam_qc.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_wgs_gvcf_combine.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_wgs_haplotype_calling.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_wgs_impute.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_wgs_index.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_wgs_joint_genotyping.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_wgs_maf_missing_filter.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_wgs_markdup.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_wgs_qc.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_wgs_variant_filter.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_wgs_variant_select.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
string_api.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
validate_manifest.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00