Zobrazeno 1 - 10
of 668
pro vyhledávání: '"batch effect"'
Publikováno v:
Genome Biology, Vol 25, Iss 1, Pp 1-29 (2024)
Abstract Increasingly, scRNA-Seq studies explore cell populations across different samples and the effect of sample heterogeneity on organism’s phenotype. However, relatively few bioinformatic methods have been developed which adequately address th
Externí odkaz:
https://doaj.org/article/63f57038731f451190d9327b3cc02021
Autor:
Richard Van, Daniel Alvarez, Travis Mize, Sravani Gannavarapu, Lohitha Chintham Reddy, Fatma Nasoz, Mira V. Han
Publikováno v:
BMC Bioinformatics, Vol 25, Iss 1, Pp 1-22 (2024)
Abstract Background RNA sequencing combined with machine learning techniques has provided a modern approach to the molecular classification of cancer. Class predictors, reflecting the disease class, can be constructed for known tissue types using the
Externí odkaz:
https://doaj.org/article/1f53e28f104c412b8a2fb317eca5b915
Publikováno v:
Advanced Science, Vol 11, Iss 31, Pp n/a-n/a (2024)
Abstract In recent years, the integration of single‐cell multi‐omics data has provided a more comprehensive understanding of cell functions and internal regulatory mechanisms from a non‐single omics perspective, but it still suffers many challe
Externí odkaz:
https://doaj.org/article/98e6088521e44117aefc1ba90428a549
Publikováno v:
Advanced Science, Vol 11, Iss 29, Pp n/a-n/a (2024)
Abstract Numerous single‐cell transcriptomic datasets from identical tissues or cell lines are generated from different laboratories or single‐cell RNA sequencing (scRNA‐seq) protocols. The denoising of these datasets to eliminate batch effects
Externí odkaz:
https://doaj.org/article/aa22a46114ce47659d45ec869977b01a
Autor:
Matteo Scanu, Federica Del Chierico, Riccardo Marsiglia, Francesca Toto, Silvia Guerrera, Giovanni Valeri, Stefano Vicari, Lorenza Putignani
Publikováno v:
Biomedicines, Vol 12, Iss 10, p 2350 (2024)
Background: To date, there have been numerous metataxonomic studies on gut microbiota (GM) profiling based on the analyses of data from public repositories. However, differences in study population and wet and dry pipelines have produced discordant r
Externí odkaz:
https://doaj.org/article/6e77aa62b9c640e48291d1b9dfef860c
Publikováno v:
Frontiers in Genetics, Vol 15 (2024)
MicroRNAs (miRNAs) are promising biomarkers for the early detection of disease, and many miRNA-based diagnostic models have been constructed to distinguish patients and healthy individuals. To thoroughly utilize the miRNA-profiling data across differ
Externí odkaz:
https://doaj.org/article/6a0ff5b3db07460ba8df22ccd0d7270f
Autor:
Ying Yu, Naixin Zhang, Yuanbang Mai, Luyao Ren, Qiaochu Chen, Zehui Cao, Qingwang Chen, Yaqing Liu, Wanwan Hou, Jingcheng Yang, Huixiao Hong, Joshua Xu, Weida Tong, Lianhua Dong, Leming Shi, Xiang Fang, Yuanting Zheng
Publikováno v:
Genome Biology, Vol 24, Iss 1, Pp 1-26 (2023)
Abstract Background Batch effects are notoriously common technical variations in multiomics data and may result in misleading outcomes if uncorrected or over-corrected. A plethora of batch-effect correction algorithms are proposed to facilitate data
Externí odkaz:
https://doaj.org/article/12d1f02d68834a36afdf46f129f91b1b
Autor:
Yujin Jang, Hye-Won Na, Dong Yeop Shin, Jun Lee, Jun Pyo Han, Hyun Soo Kim, Su Ji Kim, Eun-Jeong Choi, Charles Lee, Yong Deog Hong, Hyoung-June Kim, Young Rok Seo
Publikováno v:
Frontiers in Public Health, Vol 12 (2024)
BackgroundUltraviolet B (UVB) from sunlight represents a major environmental factor that causes toxic effects resulting in structural and functional cutaneous abnormalities in most living organisms. Although numerous studies have indicated the biolog
Externí odkaz:
https://doaj.org/article/68c5d9eefa724e088e724fee444994f6
Autor:
Jianjiang Hu, Xavier Serra‐Picamal, Gert‐Jan Bakker, Marleen Van Troys, Sabina Winograd‐Katz, Nil Ege, Xiaowei Gong, Yuliia Didan, Inna Grosheva, Omer Polansky, Karima Bakkali, Evelien Van Hamme, Merijn van Erp, Manon Vullings, Felix Weiss, Jarama Clucas, Anna M Dowbaj, Erik Sahai, Christophe Ampe, Benjamin Geiger, Peter Friedl, Matteo Bottai, Staffan Strömblad
Publikováno v:
Molecular Systems Biology, Vol 19, Iss 6, Pp 1-15 (2023)
Abstract High‐content image‐based cell phenotyping provides fundamental insights into a broad variety of life science disciplines. Striving for accurate conclusions and meaningful impact demands high reproducibility standards, with particular rel
Externí odkaz:
https://doaj.org/article/732ee8bfa8294913a63eccb0f9aa6998
Autor:
Patrick M. Carry, Tim Vigers, Lauren A. Vanderlinden, Carson Keeter, Fran Dong, Teresa Buckner, Elizabeth Litkowski, Ivana Yang, Jill M. Norris, Katerina Kechris
Publikováno v:
BMC Bioinformatics, Vol 24, Iss 1, Pp 1-18 (2023)
Abstract Background We developed a novel approach to minimize batch effects when assigning samples to batches. Our algorithm selects a batch allocation, among all possible ways of assigning samples to batches, that minimizes differences in average pr
Externí odkaz:
https://doaj.org/article/f5f3161d1212472ba1fb4cc3ce02231b