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Plantphonedb github

WebEdit on GitHub References We manually reviewed and confirmed 23 peer-reviewed publications and 4 preprints, and collected the information of 29 scRNA-seq datasets, including ~560,000 cells of 15 tissues from 5 plant species, including Arabidopsis thaliana, Oryza sativa, Populus alba x Populus glandulosa, Solanum lycopersicum and Zea mays. WebCCI_circle: Network viewing of cell-cell communication CCI_network: Network viewing of cell-cell communication heatmap_count: The number of ligand-receptor interactions between pairwise... LR_pathway: Construction of intracellular signaling pathway LRscore: Score ligand-receptor interactions LRTargetFisher: Functional category enrichment …

GitHub - Teichlab/cellphonedb

WebJul 16, 2024 · At the PlantPhoneDB web interface, the processed datasets and results can be searched, browsed, and downloaded. To uncover novel cell–cell communication events in plants, we applied the PlantPhoneDB R package on GSE121619 dataset to infer significant cell–cell interactions of heat-shocked root cells in Arabidopsis thaliana. WebAlso, we developed a PlantPhoneDB R package, which not only provided optional four scoring approaches that calculate interaction scores of ligand-receptor pairs between cell … nick jr face balloon trick https://turbosolutionseurope.com

Overview of PlantGSAD functions. (A) Example of gene

WebDownload scientific diagram Overview of PlantGSAD functions. (A) Example of gene search results in PlantGSAD. In the first column, the background color represents the gene set category. (B) Gene ... WebJan 2, 2024 · PlantPhoneDB in R Package index Search the Jasonxu0109/PlantPhoneDB package Vignettes README.md Functions 12 Source code 5 Man pages 6 CCI_circle: … WebJan 2, 2024 · lr: A data frame of the ligand-receptor interactions. objs: object Seurat object. CellA: Ligands cell. CellB: Receptors cell. neighbor: Represents the second-order neighbors of ligand-receptor pair in the signaling network.Default is 2. novo 2 charging cable

PlantPhoneDB: A manually curated pan-plant database of ligand …

Category:Transcriptional activity of the Arabidopsis genes playing a major ...

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Plantphonedb github

GitHub - Teichlab/cellphonedb

WebJan 7, 2024 · Here, we used single-cell RNA sequencing to investigate BS differentiation in C4maize (Zea mays L.) plants. Abaxial BS (abBS) cells of rank-2 intermediate veins specifically expressed three SWEET sucrose uniporters (SWEET13a, b, and c) and UmamiT amino acid efflux transporters. SWEET13a, b, cmRNAs were also detected in the phloem … WebDec 9, 2024 · CellPhoneDB is a publicly available repository of curated receptors, ligands and their interactions. Subunit architecture is included for both ligands and receptors, …

Plantphonedb github

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WebJan 2, 2024 · expr: A data frame or matrix of n rows (genes) and m columns (cells) normalized by SCTransform(). LRdb: A dataset with ligand-receptor pairs, such as LR_pair_ath.RDa.

WebJan 2, 2024 · Functional category enrichment analysis Description. Functional category enrichment analysis Usage LRTargetFisher(Targets, GeneSets, TotalGene) Arguments WebAs a result, the PlantPhoneDB predicted the actively communicating AT1G28290‐AT2G14890 ligand‐receptor pair in Atrichoblast‐Cortex cell pair in Arabidopsis thaliana. Importantly, the ...

WebOct 31, 2024 · PlantPhoneDB: A manually curated pan-plant database of ligand-receptor pairs infers cell-cell communication. ( Plant Biotechnology Journal ; Impact Factor 13.263 … WebAug 12, 2024 · PlantPhoneDB v1.0.0 Pre-release. A manually curated pan-plant database of ligand-receptor pairs infers cell-cell communication. Assets 5.

WebAbout — PlantPhoneDB-Tutorial v1.0.0 documentation PlantPhoneDB-Tutorial latest Overview Home Search Explorer Download References Document About Case Studies …

WebIn conclusion, PlantPhoneDB provided researchers with an integrated resources to infer cell-cell communication from scRNA-seq datasets. COLLEGE OF THE ENVIRONMENT & ECOLOGY, XIAMEN UNIVERSITY... nick jr face big mouthWebAug 7, 2024 · 从结果可以看出，PlantPhoneDB可以预测出有显著通讯活性的AT1G28290-AT2G14890配体-受体互作对，该配体-受体互作对所调控的靶基因富集到核糖体通路。 热胁迫可能会引起核糖体暂停现象，这种热触发的 mRNA 降解似乎是植物在慢性热胁迫下适应和生存所必需的。 novo 2 pod compatible with novo 3WebRecent single-cell RNA-sequencing technologies have enabled the detection of CCIs and related ligand-receptor (L-R) gene expression simultaneously. However, previous data analysis methods have... nick jr face bouncesWebthe PlantPhoneDB predicted the actively communicating AT2G14890 AT1G28290ligand-receptor - pair in Atrichoblast- Cortex cell pair in Arabidopsis thalianaImportantly, the downstream target . novo 2 white light meaningWebCase Studies — PlantPhoneDB-Tutorial v1.0.0 documentation Case Studies Edit on GitHub Case Studies Case1.ipynb was used to infer cell-cell communications from scRNA-seq datasets processed by using_example.ipynb. Case 1. Significant cell-cell interactions of Heat-Shocked Root Cells in Arabidopsis thaliana Case 2. nick jr face blueWebOct 31, 2024 · PlantPhoneDB: a manually curated pan-plant database of ligand-receptor pairs infers cell-cell communication. Getting started README.md Browse package … nick jr facebook twitterWebPlantPhoneDB Documentation!¶ Welcome! This is the documentation for PlantPhoneDB, a manually curated pan-plant database of ligand-receptor pairs infers cell-cell … nick jr face bouncing ball