Single-cell mitophagy patterns within the tumor microenvironment modulate intercellular communication, impacting the progression and prognosis of hepatocellular carcinoma by Zhengyan Li, Wei Chen, Shu Yao, Zuxiang Peng, Hongming Liu, Yongliang Tang, Yi Feng

“…Cell-to-cell communication was analyzed using the CellChat package, and pseudotime trajectory analysis was performed using the Monocle package. Gene regulatory networks were investigated with the SCENIC package, and survival analyses were conducted with mitophagy-related signatures.ResultsHCC samples analysis identified 22 clusters, including 7 principal cell types. …”
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Acute Attack of Pseudogout with the Wide Lesion in Lumbar Spondylolytic Spondylolisthesis by Hironari Kaneyama, Yuichiro Morishita, Osamu Kawano, Takuaki Yamamoto, Takeshi Maeda

“…Based on polarized light microscopy, which revealed monocle or triclinic intracellular crystals with a positive birefringence, the patient was diagnosed with pseudogout of the lumbar spine. …”
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Single-cell RNA sequencing revealed PPARG promoted osteosarcoma progression: based on osteoclast proliferation by Lei Sun, Jinhao Zhang, Zhikai Xiahou, Zhenzhen Zhao, Yanchen Liang

“…Therefore, we conducted a detailed study of osteoclasts at the single cell level, aiming to find new OS therapeutic targets to prevent tumor progression and local spread.MethodsWe analyzed the single-cell sequencing data of OS patients and usedMonocle2, Cytotrace, and Slingshot software to analyze the pseudo-sequential trajectory during OS progression. …”
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A single-cell transcriptome analysis reveals astrocyte heterogeneity and identifies CHI3L1 as a diagnostic biomarker in Parkinson's disease by Zhongying Gong, Dan Guo, Yufeng Lin, Zhiwei Liu, Mengdi Lv, Xinxin Liu, Yang Yao, Sijia Wang, Yuan Wang, Zhiyun Wang

“…The differentiation trajectory of astrocyte subtypes was explored using Monocle2. Inflammatory response scores were determined using AUCell. …”
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Single-Cell Transcriptome Analysis Reveals Different Immune Signatures in HPV- and HPV + Driven Human Head and Neck Squamous Cell Carcinoma by Simin Li, Yang Wang, Rui Sun, Debora Franceschi, Hongying Pan, Chenxuan Wei, Anthony Chukwunonso Ogbuehi, Bernd Lethaus, Vuk Savkovic, Sebastian Gaus, Rüdiger Zimmerer, Dirk Ziebolz, Gerhard Schmalz, Xiao Jiang

“…Single-cell pseudotime trajectories were constructed with MONOCLE (version 2.6.4). Cell-cell interactions were analyzed with CellChat R package. …”
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Characterizing tumor biology and immune microenvironment in high-grade serous ovarian cancer via single-cell RNA sequencing: insights for targeted and personalized immunotherapy st... by Fu Zhao, Fu Zhao, Xiaojing Jiang, Yumeng Li, Tianjiao Huang, Zhikai Xiahou, Wenyang Nie, Qian Li

“…InferCNV identified malignant epithelial cells, while Monocle, Cytotrace, and Slingshot software inferred subtype differentiation trajectories. …”
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Investigating intra‐tumoural heterogeneity and microenvironment diversity in primary cardiac angiosarcoma through single‐cell RNA sequencing by Jingyuan Huo, Zhen Wang, Wenting Zhao, Miao Chen, Haoyang Li, Fengpu He, Xiao Tian, Yaqi Ma, Firyuza Husanova, Liang Ma, Yiming Ni, Hongda Ding, Weidong Li, Hongfei Xu

“…Bioinformatic analyses, including Cell Ranger, Seurat, Monocle2, hdWGCNA, SCENIC and NicheNet, were utilized to identify distinct cell populations, transcriptional patterns, and co‐regulating gene modules. …”
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