# OmicVerse Docs Checklist 说明: - 只统计 `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs` 下的 OmicVerse notebook。 - `[x]` 表示我已经能确认它已被处理过，或在现有 skill 映射中有明确对应。 - `[ ]` 表示未确认已处理，保守留空。 ## Tutorials-bulk - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-bulk/t_bulk_combat.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-bulk/t_decov_bulk.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-bulk/t_deg.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-bulk/t_deseq2.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-bulk/t_mapping_STAR.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-bulk/t_mapping_kbpython.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-bulk/t_network.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-bulk/t_tcga.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-bulk/t_wgcna.ipynb` ## Tutorials-bulk2single - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-bulk2single/t_bulk2single.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-bulk2single/t_bulktrajblend.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-bulk2single/t_single2spatial.ipynb` ## Tutorials-llm - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-llm/ov_agent_ten_task_suite.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-llm/t_cellplm.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-llm/t_dr.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-llm/t_fm.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-llm/t_fm_aidocell.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-llm/t_fm_atacformer.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-llm/t_fm_cell2sentence.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-llm/t_fm_cellfm.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-llm/t_fm_chatcell.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-llm/t_fm_genecompass.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-llm/t_fm_genept.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-llm/t_fm_langcell.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-llm/t_fm_nicheformer.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-llm/t_fm_pulsar.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-llm/t_fm_scbert.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-llm/t_fm_sccello.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-llm/t_fm_scmulan.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-llm/t_fm_scplantllm.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-llm/t_fm_scprint.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-llm/t_fm_tabula.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-llm/t_fm_tgpt.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-llm/t_geneformer.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-llm/t_ov_agent_pbmc3k.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-llm/t_scfoundation.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-llm/t_scgpt.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-llm/t_uce.ipynb` ## Tutorials-plotting - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-plotting/t_palette.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-plotting/t_visualize_bulk.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-plotting/t_visualize_colorsystem.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-plotting/t_visualize_single.ipynb` ## Tutorials-single - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_alignment_1k.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_alignment_velocity.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_anno_noref.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_anno_ref.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_anno_trans.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_aucell.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_cellanno.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_cellfate.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_cellfate_gene.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_cellfate_genesets.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_cellmatch.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_cellphonedb.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_cellvote_pbmc3k.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_cluster.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_cnmf.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_cytotrace.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_deg_single.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_gptanno.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_lazy.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_metacells.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_metatime.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_mofa.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_mofa_glue.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_nocd.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_preprocess.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_preprocess_cpu.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_preprocess_gpu.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_scdeg.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_scdrug.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_scenic.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_scmulan.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_simba.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_single_batch.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_stavia.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_tosica.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_traj.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_via.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_via_velo.ipynb` ## Tutorials-space - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-space/t_cellpose.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-space/t_cluster_space.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-space/t_commot_flowsig.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-space/t_crop_rotate.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-space/t_decov.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-space/t_flashdeconv.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-space/t_gaston.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-space/t_mapping.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-space/t_nanostring_preprocess.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-space/t_slat.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-space/t_spaceflow.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-space/t_stagate.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-space/t_staligner.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-space/t_starfysh.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-space/t_starfysh_new.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-space/t_stt.ipynb` - [ ] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-space/t_visium_hd_preprocess.ipynb` ## Tutorials-velo - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-velo/t_alignment_velocity.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-velo/t_graphvelo.ipynb` - [x] `/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-velo/t_velo.ipynb`