2024 Plantphonedb github

Plantphonedb github

Author: ptki

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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. 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.

PlantPhoneDB: A manually curated pan-plant database of …

WebRecent 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... 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. stealer download

Case Studies — PlantPhoneDB-Tutorial v1.0.0 documentation

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. WebOct 31, 2024 · PlantPhoneDB: a manually curated pan-plant database of ligand-receptor pairs infers cell-cell communication. Getting started README.md Browse package … 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 … stealer disease

Document — PlantPhoneDB-Tutorial v1.0.0 documentation - Read …

Results of scTensor for an empirical dataset (NonMyocyte) (a) …

WebAs a result, the PlantPhoneDB predicted the actively communicating AT1G28290‐AT2G14890 ligand‐receptor pair in Atrichoblast‐Cortex cell pair in Arabidopsis thaliana. Importantly, the ... 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. stealer of secretsWebPlantPhoneDB Documentation!¶ Welcome! This is the documentation for PlantPhoneDB, a manually curated pan-plant database of ligand-receptor pairs infers cell-cell … stealer the boyz

"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... " - Plantphonedb github

Plantphonedb github

PlantPhoneDB Documentation! — PlantPhoneDB-Tutorial v1.0.0 …

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. 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 · 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 … WebClone via HTTPS Clone with Git or checkout with SVN using the repository’s web address.

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

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...

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 · PlantPhoneDB in R Package index Search the Jasonxu0109/PlantPhoneDB package Vignettes README.md Functions 12 Source code 5 Man pages 6 CCI_circle: … stealer of souls skyrimWebJan 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 … stealer the boyz lyricsWebthe PlantPhoneDB predicted the actively communicating AT2G14890 AT1G28290ligand-receptor - pair in Atrichoblast- Cortex cell pair in Arabidopsis thalianaImportantly, the downstream target . stealer seven joseon coinsWebJul 30, 2024 · Europe PMC is an archive of life sciences journal literature. stealers synonym stealer of soulsWebAug 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。 stealers wheel lead singerWebDownload 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 ... stealin all my dreams