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sj b8be4e4831 Merge branch 'master' into wip/qa7920-rag-stream
2026-08-21 11:41:16 +08:00
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bge-m3-model
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
findFile
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
legacy_startup
fix(runtime): standardize 9000 startup and isolate project services
2026-08-10 10:57:49 +08:00
pep_v2
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
tree_motif_domain_structure.R
Initial commit: PlantAI-dev
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vcf
Initial commit: PlantAI-dev
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add_rag_to_identify.py_
Initial commit: PlantAI-dev
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audit_extension_stages.py
Initial commit: PlantAI-dev
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build_faiss.sh
Initial commit: PlantAI-dev
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calculate_fpkm_tpm_simple.R
Initial commit: PlantAI-dev
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calculate_fpkm_tpm.R
Initial commit: PlantAI-dev
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check_autofill_regression.py
Initial commit: PlantAI-dev
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check_project_environment.sh
Initial commit: PlantAI-dev
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check_rnaseq_confirm_params.js
Initial commit: PlantAI-dev
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check_rnaseq_strandness.py
Initial commit: PlantAI-dev
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check_subfamily_evidence_scope.py
Initial commit: PlantAI-dev
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collect_conversion_publication_figures.py
Initial commit: PlantAI-dev
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combine_hmm_blast.py
Initial commit: PlantAI-dev
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combo_tree_motif_structure_domain_panel_test.R
Initial commit: PlantAI-dev
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combo_tree_motif_structure_domain.R
Initial commit: PlantAI-dev
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cross_stress_analysis.py
Initial commit: PlantAI-dev
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download_planttfdb_motifs.py
Initial commit: PlantAI-dev
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draw_enrich_expression.R
Initial commit: PlantAI-dev
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draw_expression.R
Initial commit: PlantAI-dev
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draw_motif_seqlogo.R
Initial commit: PlantAI-dev
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draw_ppi_network.R
Initial commit: PlantAI-dev
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draw_rnaseq_expression.R
Initial commit: PlantAI-dev
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eggnog_crawler.py
Initial commit: PlantAI-dev
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extension_stage_benchmark_report.py
Initial commit: PlantAI-dev
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extension_stage_golden_validate.py
Initial commit: PlantAI-dev
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extension_stage_template_cases.py
Initial commit: PlantAI-dev
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extension_stage_template_validate.py
Initial commit: PlantAI-dev
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fasta_pI_mw.R
Initial commit: PlantAI-dev
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fetch_gene2go_bioc.R
Initial commit: PlantAI-dev
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fix_all_syntax.py
Initial commit: PlantAI-dev
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gene_highlight_jcvi.py
Initial commit: PlantAI-dev
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GeneFamily_stat.py
Initial commit: PlantAI-dev
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get_dataset_color.py
Initial commit: PlantAI-dev
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get_dataset_symbol.py
Initial commit: PlantAI-dev
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get_mapchart_tandem.py
Initial commit: PlantAI-dev
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get_mcscanx_circos.py
Initial commit: PlantAI-dev
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get_meme_pos.py
Initial commit: PlantAI-dev
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get_Plant_mPLoc_out.py
Initial commit: PlantAI-dev
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gff_filter_bymRNAID.py
Initial commit: PlantAI-dev
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gff_filter_longest.py
Initial commit: PlantAI-dev
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interspecies_tree.R
Initial commit: PlantAI-dev
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karyogram_gene_family.R
Initial commit: PlantAI-dev
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kegg.R
Initial commit: PlantAI-dev
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map_data_ids.py
Initial commit: PlantAI-dev
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map_fasta_ids.py
Initial commit: PlantAI-dev
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map_gff_ids.py
Initial commit: PlantAI-dev
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motree_py.py
Initial commit: PlantAI-dev
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MOTree.pm
Initial commit: PlantAI-dev
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msa_figure_from_aligned.R
Initial commit: PlantAI-dev
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msa_figure.mattf.R
Initial commit: PlantAI-dev
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msa_figure.R
Initial commit: PlantAI-dev
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multi_species_integration.py
Initial commit: PlantAI-dev
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plot_interspecies_synteny.R
Initial commit: PlantAI-dev
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plot_pop_ld_decay.py
Initial commit: PlantAI-dev
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plot_rnaseq_go_enrichment.R
Initial commit: PlantAI-dev
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plot_structure.R
Initial commit: PlantAI-dev
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plot_tree.Huihuai.R
Initial commit: PlantAI-dev
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plot_tree.py
Initial commit: PlantAI-dev
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plot_tree.R
Initial commit: PlantAI-dev
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pop_snp_density_cmplot.R
Initial commit: PlantAI-dev
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prefix_reference_gff.py
Initial commit: PlantAI-dev
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prepare_input.py
Initial commit: PlantAI-dev
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prepare_string_species_snapshot.py
Initial commit: PlantAI-dev
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promoter_analysis_complete.R
Initial commit: PlantAI-dev
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promoter_custom_plot.R
Initial commit: PlantAI-dev
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promoter_element_categories.md
Initial commit: PlantAI-dev
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promoter_position_distribution.R
Initial commit: PlantAI-dev
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promoter_v4_final.R
Initial commit: PlantAI-dev
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promoter_v5_fused_heatmap.R
Initial commit: PlantAI-dev
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promoter_v6_combined.R
Initial commit: PlantAI-dev
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promoter_visualization_enhanced_v2.R
Initial commit: PlantAI-dev
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promoter_visualization_enhanced_v3.R
Initial commit: PlantAI-dev
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promoter_visualization_enhanced_v4.R
Initial commit: PlantAI-dev
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promoter_visualization_enhanced.R
Initial commit: PlantAI-dev
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pysam_bcftools.py
Initial commit: PlantAI-dev
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qa_v1_1_73_server.py
wip: qa7920 sidecar + rag stream timeout
2026-08-21 11:04:28 +08:00
reference_classification_from_tree.py
Initial commit: PlantAI-dev
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render_extension_publication_figures.py
Initial commit: PlantAI-dev
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reorganize_workspace.py
Initial commit: PlantAI-dev
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repair_gwas_asaw_tools.py
Initial commit: PlantAI-dev
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rnaseq_expression_plot_prototype.R
Initial commit: PlantAI-dev
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run_blast_pipeline.py
Initial commit: PlantAI-dev
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run_extension_archetype_experiments.py
Initial commit: PlantAI-dev
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run_extension_p0_fixture_experiments.py
Initial commit: PlantAI-dev
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run_extension_publication_experiments.py
Initial commit: PlantAI-dev
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run_extension_tri_chain_evidence_experiments.py
Initial commit: PlantAI-dev
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run_finalize_members.py
Initial commit: PlantAI-dev
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run_gwas_api20_benchmark.py
Initial commit: PlantAI-dev
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run_gwas_extension_stage_experiment.py
Initial commit: PlantAI-dev
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run_gwas_publication_experiments.py
Initial commit: PlantAI-dev
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run_hmm_pipeline.py
Initial commit: PlantAI-dev
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run_identify.py
Initial commit: PlantAI-dev
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run_motif.py
Initial commit: PlantAI-dev
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run_msa_figure.py
Initial commit: PlantAI-dev
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run_phylogeny.py
Initial commit: PlantAI-dev
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run_summary.py
Initial commit: PlantAI-dev
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run_vcf10_threshold_adapter_conversion_test.py
Initial commit: PlantAI-dev
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run_vcf_api20_benchmark.py
Initial commit: PlantAI-dev
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sim_verify_go_only_stage.py
Initial commit: PlantAI-dev
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sim_verify_three_stages.py
Initial commit: PlantAI-dev
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sort_fasta_by_ids.py
Initial commit: PlantAI-dev
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start_qa_v1_1_73_7920.sh
wip: qa7920 sidecar + rag stream timeout
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subfamily_palette.R
Initial commit: PlantAI-dev
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subfamliy_blast.py
Initial commit: PlantAI-dev
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test_deeptmhmm_topology_plot.py
Initial commit: PlantAI-dev
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test_interspecies_multi_ref_plan_b.py
Initial commit: PlantAI-dev
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test_ortholog_revision_verify.py
Initial commit: PlantAI-dev
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test_promoter_viz_output_path.py
Initial commit: PlantAI-dev
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test_rnaseq_de_to_go_enrich_simulated_full.py
Initial commit: PlantAI-dev
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test_rnaseq_enrich_background_recovery_flow.py
Initial commit: PlantAI-dev
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test_rnaseq_go_kegg_annotation_agent_flow.py
Initial commit: PlantAI-dev
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test_rnaseq_multiagent_linkage.py
Initial commit: PlantAI-dev
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test_subcellular_heatmap_plot.py
Initial commit: PlantAI-dev
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tf_expression_clustering.py
Initial commit: PlantAI-dev
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tf_family_analysis.py
Initial commit: PlantAI-dev
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tiqu_miaoshuwenjian.py
Initial commit: PlantAI-dev
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tree_domain.R
Initial commit: PlantAI-dev
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tree_motif.R
Initial commit: PlantAI-dev
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tree_plot.R
Initial commit: PlantAI-dev
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tximport_abundance.R
Initial commit: PlantAI-dev
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validate_qa_v1_1_73_sidecar.sh
wip: qa7920 sidecar + rag stream timeout
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wolfpsort_batch.py
Initial commit: PlantAI-dev
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