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evolved-nanno Public
Code to analyze genomic variation bewteen evolved strains of Nannochloropsis
UpdatedJun 3, 2025 -
rhythmic-potato Public
Cis-element enrichment in domesticated and wild potato
Jupyter Notebook UpdatedMay 21, 2025 -
photorespiration-omics Public
Using transcriptomics and proteomics to study photorespiration
Jupyter Notebook UpdatedMay 19, 2025 -
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deuteration-utils Public
Utility code for input data formatting for the DeuteRater tool
Python UpdatedApr 14, 2025 -
dygiepp Public
Forked from dwadden/dygieppSpan-based system for named entity, relation, and event extraction.
Python MIT License UpdatedJan 8, 2025 -
literature-genes Public
Code to identify gene candidates involved in desiccation tolerance from the literature
Jupyter Notebook UpdatedJan 8, 2025 -
ontogpt Public
Forked from monarch-initiative/ontogptLLM-based ontological extraction tools, including SPIRES
Jupyter Notebook BSD 3-Clause "New" or "Revised" License UpdatedJan 8, 2025 -
STHN Public
Forked from celi52/STHNSTHN: Simplifying Temporal Heterogeneous Network for Continuous-Time Link Prediction [CIKM 2023]
Python UpdatedMay 31, 2024 -
desiccation-network Public
Code for the project Drying to Connect: A bibliometric analysis of desiccation tolerance research across the kingdoms of life.
Jupyter Notebook UpdatedMay 30, 2024 -
pickle-corpus-code Public
Code for the manuscript "In a PICKLE: Entity and relation annotation guidelines for the molecular plant sciences"
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forum-lesson-plan Public
Lesson 6 for Foundations in Computational Plant Science (NRT-IMPACTS)
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obie-wan Public archive
Improved entity and relation extraction in the plant sciences through ontology-based information extraction
Jupyter Notebook UpdatedNov 29, 2023 -
taxonerd Public
Forked from nleguillarme/taxonerdTaxoNERD : recognizing taxonomic entities using deep models
Jupyter Notebook MIT License UpdatedSep 7, 2023 -
lm-evaluation-harness Public
Forked from EleutherAI/lm-evaluation-harnessA framework for few-shot evaluation of autoregressive language models.
Python MIT License UpdatedMay 16, 2023 -
multi-omics Public
Code for multi-omic deep learning integration project
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knowledge-graph Public
Code exploring the creation of knowledge graphs from plant science papers
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msu-datathon-4-justice Public
MSU team's code for the QSIDE Datathon4Justice
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goatools Public
Forked from tanghaibao/goatoolsPython library to handle Gene Ontology (GO) terms
Python BSD 2-Clause "Simplified" License UpdatedOct 26, 2021 -
PURE Public
Forked from princeton-nlp/PURENAACL'2021: A Frustratingly Easy Approach for Entity and Relation Extraction
Python MIT License UpdatedSep 13, 2021 -
plant-history Public
Using NLP techniques to explore the prevalance of topics of study in the plant sciences over the last 100 years
UpdatedMar 24, 2021 -
ML-Pipeline Public
Forked from azodichr/ML-PipelineShiu Lab code base for Machine Learning implemented in SciKit-Learn
Python UpdatedJan 31, 2021 -
yeast-interpretability Public
Using machine learning interpretability methods to study yeast genetic interaction
Python UpdatedNov 10, 2020 -
bratiaa Public
Forked from kldtz/bratiaaInter-annotator agreement for Brat annotation projects
Python MIT License UpdatedOct 1, 2020 -
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treeinterpreter Public
Forked from andosa/treeinterpreterPython BSD 3-Clause "New" or "Revised" License UpdatedJun 18, 2020
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