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Cell Biology Bioinformatics Automation in Bioinformatics Introduction Recent advancements in single-cell RNA sequencing (scRNA-seq) have furthered the understanding of heterogeneous cell compositions in complex tissues through the characterization of different cell types based on gene expression levels, thus ...
Exorcise focuses CRISPR experiments towards the genome of the cell line under investigation. Exorcise can be applied at the library design stage or the analysis stage and allows post
Untargeted metabolomics experiments rely on spectral libraries for structure annotation, but, typically, only a small fraction of spectra can be matched. Previous in silico methods search in structure databases but cannot distinguish between correct and incorrect annotations. Here we introduce the COSMIC ...
Transcriptome annotation allows us to understand which genes are being expressed in a particular cell or tissue at a given time, and how the expression of these genes contributes to the overall biology of the cell or tissue. Two main types of annotation are used: Homology-based annotation ...
Act like an expert immunologist and give me the cell type annotation for this cluster. ") Thinking… ## ### Step 1 : ## ## Here is the first step of my reasoning chain: ## ## ``` ## { ## "title": "Initial Problem Decomposition", ## "content": "Given the list of up-...
In particular, a number of studies have shown that an increased fetal hemoglobin (HbF; α2γ2) response in conjunction with either sickle cell disease or β-thalassemia has an ameliorating effect on the clinical disease [3, 4]. This has prompted intensive investigations on γ-globin gene ...
of cell types across complex annotation hierarchies. To demonstrate the power ofdevCellPy, we construct a murine cardiac developmental atlas from published datasets encompassing 104,199 cells from E6.5-E16.5 and traindevCellPyto generate a cardiac prediction algorithm. Using this algorithm, we ...
These databases act primarily as archival storage of sequence information. Consequently, each entry is owned by the sequence provider and integrating annotation information is, by design, nearly impossible. A number of specialized databases have developed to serve a curatorial role within particular ...
Reference epigenomes enable comprehensive annotations of dynamic non-coding regulatory and transcribed elements across hundreds of human cell types and tissues