Conditional sQTL analysis was done by forward stepwise regression followed by a backward selection step. The gene-level significance threshold was set to the maximum beta-adjusted P value over all sGenes in a given cell type. Scanning for cis-sQTLs using QTLtools was performed to correct for ...
Specifically, they are selected within each sample separately and then merged to avoid the selection of batch-specific genes. scAEspy is used to reduce the HVG space (k dimensions), and the obtained latent space can be (i) used to calculate a t-SNE space, (ii) corrected by Harmony, and...
Single-cell assay for transposase-accessible chromatin by sequencing (scATAC-seq) has emerged as a powerful tool for dissecting regulatory landscapes and cellular heterogeneity. However, an exploration of systemic biases among scATAC-seq technologies has remained absent. In this study, we benchmark the...
MinKNOW carries out several core tasks—data acquisition; real-time analysis and feedback; data streaming while providing device control (including run parameter selection); as well as sample identification and tracking—thus ensuring that the platform chemistry performs correctly in processing the ...
Inference of chromosome selection parameters and missegregation rate in cancer from DNA-sequencing data ArticleOpen access31 July 2024 18 July 2024 Introduction DNA replication and cell cycle regulation are frequently disrupted as part of a cancer’s progression toward uncontrolled proliferation1,2,3. ...
scAbsolute: measuring single-cell ploidy and replication status ArticleOpen access04 March 2024 Inference of chromosome selection parameters and missegregation rate in cancer from DNA-sequencing data ArticleOpen access31 July 2024 Introduction DNA replication and cell cycle regulation are frequently disrupted...
cDNA size-selection prior to concatemer formation. 5) PCR using primers containing known reverse-complement barcodes with uracil incorporation ("dU”), followed by USER digestion and ligation to form the concatemer array. 6) Samples undergo PacBio SMRTbell prep, sequencing, and PacBio primary ...
(Top) The same network as in panel b, trained with dropout on hidden nodes. Dropout nodes are randomly selected at each training iteration. (Bottom) Learning with dropout results in robust and highly correlated weights (inset) for the two redundant nodes.dNode weights of weakly and strongly ...
datasets. Third, we provide some original implementations of some PCA algorithms and utility functions for quality control (QC), filtering, and feature selection. All commands are implemented in a fast and memory-efficient Julia package. Finally, we propose guidelines for end-users and software ...
Nanopore sequencers can select which DNA molecules to sequence, rejecting a molecule after analysis of a small initial part. Currently, selection is based on predetermined regions of interest that remain constant throughout an experiment. Sequencing effo