Fungal gene predictionFungal genome annotation pipelineGenome annotationGenome assemblyRNA-seqFunGAP is a Python-wrapped fungal genome annotation pipeline running under the Linux/Unix operating system. The anno
标记基因(marker gene)的概念与差异表达(DE)基因的概念密切相关,但两个概念并不是不同义词。严格来说,标记基因选择是DE基因鉴定的一个子集,有效且有用的标记基因具有并非所有DE基因所共有的特定特征。广义上,我们将标记基因定义为可用于区分细胞亚群的基因。 文献标题及背景 A comparison of marker gene selection ...
PProdigal: Parallelized gene prediction based on Prodigal. This is just a small wrapper around the prodigal gene prediction program that splits input into chunks and processes them im parallel, since prodigal does not support multithreading by itself. The wrapper supports all command line parameters ...
📝Note:This is a revamp of the ABC codebase presented in [1]. If you wish to access that version of the ABC repo, please check outhttps://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction/tree/master. We have documented the codebase and usage inRead The Docs ...
Factor analysis decomposes single-cell gene expression data into a minimal set of gene programs that correspond to processes executed by cells in a sample. However, matrix factorization methods are prone to technical artifacts and poor factor interpretability. We address these concerns with Spectra, an...
The three other types of enhancers (closed chromatin, chromatin dependent and classical) appeared active based on the fact that inclusion of the corresponding features improved prediction of differential gene expression between GP5d and HepG2 cells (Supplementary Table 6 and Methods). Analysis of ...
perturbation condition or disease status across ten publicly available single-cell RNA sequencing datasets (see the “Methods” section, Additional file1: Table S1). Datasets were grouped into three general categories according to the prediction task. Here, we briefly introduce the datasets used in ...
Gene expression data (RNA/DNA microarray) are often used to develop such prediction models. Results The outcome of the present work is an experimental methodology to develop prediction models, based on robust gene signatures, for the classification of cigarette smoke exposure and cessation in humans...
quantified. Additionally, the 'Functional Tree' defines groups with biological meaning enhancing its utility for protein function comparison and prediction. Finally, this approach could be for function-based protein searches in databases, and for analysing the gene clusters produced by DNA array ...
For this analysis, we formulated a prediction task: Using the SV annotations as a “ground truth” labeled feature set (the gene associated with the SV is positively labeled and all other genes are negatively labeled), we measured how well we could predict the presence of an associated SV (...