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Refactor LLM interpretation with aisdk and update documentation #812

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Refactor LLM interpretation with aisdk and update documentation #812

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cb324d4
chore: update ignore files for LLM config
xiayh17 Feb 28, 2026
ce59da6
refactor: replace fanyi with aisdk and add provider support in interpret
xiayh17 Feb 28, 2026
818182e
docs: update documentation for interpret functions
xiayh17 Feb 28, 2026
a52882f
refactor: clean up and simplify print.interpretation method
xiayh17 Feb 28, 2026
056609c
refactor: migrate to aisdk structured output and update documentation
xiayh17 Feb 28, 2026
641a889
feat: Replace fanyi with aisdk for LLM-based interpretation
xiayh17 Feb 28, 2026
47160ec
fix: address R CMD check warnings and notes (undocumented args, missi…
xiayh17 Feb 28, 2026
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1 change: 1 addition & 0 deletions .Rbuildignore
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Original file line number Diff line number Diff line change
Expand Up @@ -20,3 +20,4 @@ outdated
inst/sticker
local_test
.trae
.env
5 changes: 4 additions & 1 deletion .gitignore
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Expand Up @@ -7,7 +7,10 @@ __pycache__
__init__.py
__init__.pyc
.Rproj.user
.Rhistory
.RData
*.Rproj

.vscode/
.trae

.env
7 changes: 5 additions & 2 deletions DESCRIPTION
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Expand Up @@ -39,12 +39,12 @@ Imports:
tidyr,
utils,
yulab.utils (>= 0.2.3),
ggplot2
ggplot2,
aisdk
Suggests:
AnnotationHub,
BiocManager,
DOSE,
fanyi (>= 0.1.0),
ggtangle,
readr,
org.Hs.eg.db,
Expand All @@ -60,3 +60,6 @@ biocViews: Annotation, Clustering, GeneSetEnrichment, GO, KEGG,
MultipleComparison, Pathways, Reactome, Visualization
Encoding: UTF-8
RoxygenNote: 7.3.3
Remotes:
YuLab-SMU/aisdk

8 changes: 8 additions & 0 deletions NAMESPACE
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Expand Up @@ -129,6 +129,13 @@ importFrom(GOSemSim,godata)
importFrom(GOSemSim,mgoSim)
importFrom(GOSemSim,read.blast2go)
importFrom(GOSemSim,read.gaf)
importFrom(aisdk,Agent)
importFrom(aisdk,ChatSession)
importFrom(aisdk,generate_object)
importFrom(aisdk,z_array)
importFrom(aisdk,z_enum)
importFrom(aisdk,z_object)
importFrom(aisdk,z_string)
importFrom(dplyr,arrange)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
Expand Down Expand Up @@ -173,6 +180,7 @@ importFrom(rlang,check_installed)
importFrom(rlang,quos)
importFrom(rlang,sym)
importFrom(stats,formula)
importFrom(stats,na.omit)
importFrom(stats,setNames)
importFrom(tidyr,gather)
importFrom(tidyr,separate)
Expand Down
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