Salmon provides fast and bias-aware quantification of transcript expression. Nat. Methods 14, 417–419 (2017). Article CAS PubMed PubMed Central Google Scholar Wolf, F. A., Angerer, P. & Theis, F. J. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol. 19, ...
The Human BioMolecular Atlas Program (HuBMAP) aims to construct a 3D Human Reference Atlas (HRA) of the healthy adult body. Experts from 20+ consortia collaborate to develop a Common Coordinate Framework (CCF), knowledge graphs and tools that describe the multiscale structure of the human body ...
We obtained post-filtered, post-doublet removal data directly from the authors47 along with author-defined cell type annotations for 113,063 cells (14 donors) sequenced with 10x 3’ end bias (reference) and a separate 25,367 cells sequenced with 10x 5’ end bias (query). For building the...
To avoid the model bias towards major class for the imbalance dataset problem, we applied the focal loss [33] to guide the model focusing more on hard, misclassified samples. The model was trained using the Adam optimizer [34] with a learning rate of 10−3. A general description of ...
dataset: To ensure that the inclusion of these samples would not bias the clustering or the gene expression patterns, we performed the following analysis. First, we analyzed the neuronal cluster distribution of each experimental condition. Overall, nuclei from the formalin and rotarod conditions ...
HSCs in the blood of patients with COVID-19 (top left) show a megakaryocyte priming bias compared with healthy cells (top right). This is quantified in the histogram from the human thymus single-cell atlas of relative HSPC contributions for different donor/patient cohorts156. A well-annotated...
To mitigate the bias in the distribution of TF expression and REs chromatin accessibility so that the PCC is comparable across different TF–RE pairs, we permute the cell barcode in the gene expression data and then calculate, generating a background PCC distribution for each TF–RE pair. We ...
5g, i.7g). However, it is not clear if all Notum- and Sall1-expressing progenitor cells always irreversibly and selectively commit to the odontoblast fate or these factors convey a strong bias towards odontoblast differentiation. This goes in-line with the previously established fact that ...
Since this might have introduced a small bias in the results, the quantitative metric errors of the MA method were reported relatively to PMI-70. Thereafter, the PMI-40 and PMI-70 datasets were used for neural network training. In the quantitative results of the 3D U-Net, the contrary was...
To minimize the bias in determining the localization patterns, each localization image was independently analyzed by two researchers. Localization patterns for 31 proteins where there was clear disagreement or insufficient signal were categorized as Ambiguous. FRAP assays were performed using a Nikon A1R-...