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
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...
the gene count for each function and color intensity reflectingp-value significance – darker hues indicate higher pathway enrichment (top10 of positive and negative NES, padj < 0.05, padj calculated by GSEApy python package, For the statistical analysis, we used thepvalue adjustment to contr...
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 efforts, thus, cannot be re-focused on molecules li...
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 ...
Here we describe cell-type-specific, sex-biased and ancestry-biased alternative splicing in ~1 M peripheral blood mononuclear cells from 474 healthy donors from the Asian Immune Diversity Atlas. We identify widespread sex-biased and ancestry-biased differential splicing, most of which is cell-...
Video S1. 63× Confocal Stack Showing CLEC7a + (Red) CX3CR1-GFP + Microglia in the P7 Cerebellum Engulfing Other Nuclei (See Also Figure 8A for a Presentative Single Plane and Figure 8B for 3D Reconstruction of a Typical Microglia Phagocytosing a Pyknotic Nucleus), Related to Figure 8...
Parameter estimation is carried out using a Markov chain Monte Carlo expectation-maximization (MCMC-EM) algorithm, and information criteria are used for model selection. Conclusions: The mixture of MPLN model is able to fit a wide range of correlation and overdispersion situations, and is suited ...
(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 ...
1. A method for filtering out erroneous sequence reads from a genomic sequence dataset, comprising: receiving, by one or more processors, the genomic sequence dataset, wherein the dataset comprises a plurality of fragment sequence reads, each with an associated barcode sequence and a unique identif...