Plantphonedb github

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August undefined, 2024

WebWith a personal account on GitHub, you can import or create repositories, collaborate with others, and connect with the GitHub community. Getting started with GitHub Team With GitHub Team groups of people can collaborate across many projects at the same time in an organization account. 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. 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. glasses malone that good

Correspondence table containing the available L-R gene

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... WebOct 31, 2024 · PlantPhoneDB: a manually curated pan-plant database of ligand-receptor pairs infers cell-cell communication. Getting started README.md Browse package … WebDownload scientific diagram Correspondence table containing the available L-R gene information for each organism For each detected CaH, gene annotation, enrichment analysis, tissue-or cell-type ... glasses magnify my eyes

Plantphonedb github

LRscore: Score ligand-receptor interactions in Jasonxu0109/PlantPhoneDB …

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: … 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, …

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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. WebPlantPhoneDB: A manually curated pan-plant database of ligand-receptor pairs infers cell-cell communication. ( Plant Biotechnology Journal ; Impact Factor 13.263 ; accepted ) …

WebJan 2, 2024 · Functional category enrichment analysis Description. Functional category enrichment analysis Usage LRTargetFisher(Targets, GeneSets, TotalGene) Arguments WebAug 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。

WebBackground: In plants, the plasma membrane is enclosed by the cell wall and anchors RLK and RLP proteins, which play a fundamental role in perception of developmental and environmental cues and are... WebPlantPhoneDB Documentation!¶ Welcome! This is the documentation for PlantPhoneDB, a manually curated pan-plant database of ligand-receptor pairs infers cell-cell …

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 …

WebEdit on GitHub. PlantPhoneDB is a ligand-receptor interactions database, which aims to infer cell-cell communications from scRNA-seq datasets in plant. We built the PlantPhoneDB … glasses make my eyes tiredWebCase 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. glasses lord of the flies symbolismWebDocument — PlantPhoneDB-Tutorial v1.0.0 documentation Document Edit on GitHub Document We provide the R script needed to reproduce the processed scRNA-seq datasets results of PlantPhoneDB. Quick Installation First, install devtools (for installing GitHub packages) if it isn’t already installed: glasses on and off memeWebAbout — PlantPhoneDB-Tutorial v1.0.0 documentation PlantPhoneDB-Tutorial latest Overview Home Search Explorer Download References Document About Case Studies … glasses look youngerWebAug 12, 2024 · PlantPhoneDB v1.0.0 Pre-release. A manually curated pan-plant database of ligand-receptor pairs infers cell-cell communication. Assets 5. glassesnow promo codeWebJan 2, 2024 · GitHub / Jasonxu0109/PlantPhoneDB / CCI_circle: Network viewing of cell-cell communication CCI_circle: Network viewing of cell-cell communication In Jasonxu0109/PlantPhoneDB: PlantPhoneDB in R View source: R/CCI_circle.r CCI_circle R Documentation Network viewing of cell-cell communication Description Network viewing … glasses liverpool streetWebAlso, we developed a PlantPhoneDB R package, which not only provided optional four scoring approaches that calculate interaction scores of ligand-receptor pairs between cell … glasses make things look smaller