clusterProfiler
- clusterProfiler
supports exploring functional characteristics of both coding and
non-coding genomics data for thousands of species with up-to-date
gene annotation.
- It provides a universal interface for gene functional annotation
from a variety of sources and thus can be applied in diverse
scenarios.
- It provides a tidy interface to access, manipulate, and visualize
enrichment results to help users achieve efficient data
interpretation
- Datasets obtained from multiple treatments and time points can be
analyzed and compared in a single run, easily revealing functional
consensus and differences among distinct conditions
For details, please visit
https://yulab-smu.top/biomedical-knowledge-mining-book/.
:writing_hand: Authors
Guangchuang YU https://yulab-smu.top
School of Basic Medical Sciences, Southern Medical University
If you use
clusterProfiler in
published research, please cite the most appropriate paper(s) from this
list:
- T Wu#, E Hu#, S Xu, M Chen, P Guo, Z Dai, T
Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo*, G
Yu*. clusterProfiler 4.0: A universal enrichment tool
for interpreting omics data. The Innovation. 2021,
2(3):100141. doi:
10.1016/j.xinn.2021.100141
- G Yu*. Gene Ontology Semantic Similarity Analysis
Using GOSemSim. In: Kidder B. (eds) Stem Cell Transcriptional
Networks. Methods in Molecular Biology. 2020, 2117:207-215.
Humana, New York, NY. doi:
10.1007/978-1-0716-0301-7_11
- G Yu*. Using meshes for MeSH term enrichment and
semantic analyses. Bioinformatics. 2018, 34(21):3766–3767.
doi:
10.1093/bioinformatics/bty410
- G Yu, QY He*. ReactomePA: an R/Bioconductor package
for reactome pathway analysis and visualization. Molecular
BioSystems. 2016, 12(2):477-479. doi:
10.1039/C5MB00663E
- G Yu*, LG Wang, and QY He*. ChIPseeker:
an R/Bioconductor package for ChIP peak annotation, comparison and
visualization. Bioinformatics. 2015, 31(14):2382-2383. doi:
10.1093/bioinformatics/btv145
- G Yu*, LG Wang, GR Yan, QY He*. DOSE: an
R/Bioconductor package for Disease Ontology Semantic and Enrichment
analysis. Bioinformatics. 2015, 31(4):608-609. doi:
10.1093/bioinformatics/btu684
- G Yu, LG Wang, Y Han and QY He*. clusterProfiler: an
R package for comparing biological themes among gene clusters.
OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.
doi: 10.1089/omi.2011.0118
- G Yu, F Li, Y Qin, X Bo*, Y Wu, S Wang*.
GOSemSim: an R package for measuring semantic similarity among GO
terms and gene products. Bioinformatics. 2010, 26(7):976-978.
doi:
10.1093/bioinformatics/btq064