SCP: Single-Cell PipelineSCP provides a comprehensive set of tools for single-cell data processing and downstream analysis.The package includes the following facilities:Integrated single-cell quality control methods. Pipelines embedded with multiple methods for normalization, feature reduction, and cell pop...
Single-cell RNA-sequencing analysis to quantify the RNA molecules in individual cells has become popular, as it can obtain a large amount of information from each experiment. We introduce UniverSC ( https://github.com/minoda-lab/universc ), a universal s
Oxford Nanopore's single cell pipeline (successor to Sockeye) with enhancements for our cluster - gandallab/wf-single-cell
pipeline steps. We find that choices of normalisation and library preparation protocols have the biggest impact on scRNA-seq analyses. Specifically, we find that library preparation determines the ability to detect symmetric expression differences, while normalisation dominates pipeline performance in ...
An overview of the single-cell pipeline is shown in Figure 1a.Fig. 1. Overview of CUT&RUNTools 2.0. (a) The workflow of single-cell data processing and analysis and (b) the genome browser tracks for the HOXB gene locus Open in new tabDownload slide...
The application of single-cell RNA sequencing (scRNA-seq) in biomedical research has advanced our understanding of the pathogenesis of disease and provided valuable insights into new diagnostic and therapeutic strategies. With the expansion of capacity f
3. 流行的分析平台也有限制。如Seurat,Scater,或者Scanpy 提供了整合的环境以发展pipeline以及囊括更大的分析工具箱(toolboxes)。然而,处于必要,这些方法都将自己限制于各自的编程语言中。语言限制也适用于目前的scRNA-seq分析,例如以下主流的分析平台: R and bioconductor tools :drisso/bioc2016singlecellandhttps://...
Analysis categoryPipelineEnvironmentDescription Overall analysis Seurat [78] R A comprehensive tool to perform QC analysis on diverse types of single-cell data. Spatial interference using in situ RNA patterns as a reference. Compatible with multimodal data.http://satijalab.org/seurat/ Scanpy [79] Py...
enabling partitioning, cell lysis, and barcoding of cellular information. These barcoded transcripts are then amplified and converted into libraries compatible with Illumina or other short-read sequencing platforms. After sequencing, the results are analyzed using the Cell Ranger pipeline and visualized us...
The burden of copy number alteration, including amplification and deletion, was measured at both the focal and arm levels using CNV data from the GISTIC 2.0 pipeline. As previously reported, we estimated the percentage of genome alteration (FGA), fraction of genomic gain (FGG), and fraction of...