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#
/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/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-bulk/t_deg.ipynb/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/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-bulk/t_network.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-bulk/t_tcga.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-bulk/t_wgcna.ipynb
Tutorials-bulk2single#
/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-bulk2single/t_bulk2single.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-bulk2single/t_bulktrajblend.ipynb/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/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-plotting/t_visualize_bulk.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-plotting/t_visualize_colorsystem.ipynb/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/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_alignment_velocity.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_anno_noref.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_anno_ref.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_anno_trans.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_aucell.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_cellanno.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_cellfate.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_cellfate_gene.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_cellfate_genesets.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_cellmatch.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_cellphonedb.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_cellvote_pbmc3k.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_cluster.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_cnmf.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_cytotrace.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_deg_single.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_gptanno.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_lazy.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_metacells.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_metatime.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_mofa.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_mofa_glue.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_nocd.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_preprocess.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_preprocess_cpu.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_preprocess_gpu.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_scdeg.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_scdrug.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_scenic.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_scmulan.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_simba.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_single_batch.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-single/t_stavia.ipynb/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#
/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-velo/t_alignment_velocity.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-velo/t_graphvelo.ipynb/Users/fernandozeng/Desktop/analysis/omicverse/omicverse_guide/docs/Tutorials-velo/t_velo.ipynb