①https://yiweiniu.github.io/blog/2019/03/ATAC-seq-data-analysis-from-FASTQ-to-peaks/ ②https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/atac-seq/tutorial.html 这两个教程非常细致地讲解了从Raw data到ATAC-seq 的peak数据的分析流程,数据处理这部分就不多赘述了,不过这...
①https://yiweiniu.github.io/blog/2019/03/ATAC-seq-data-analysis-from-FASTQ-to-peaks/ ②https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/atac-seq/tutorial.html 这两个教程非常细致地讲解了从Raw data到ATAC-seq ...
http://www.regulatory-genomics.org/hint/introduction/ http://www.regulatory-genomics.org/hint/tutorial/ 在本教程中,将展示如何使用HINT-ATAC来比较活化的转录因子的足迹变化。使用在HINT-ATAC论文中提供的数据,对比两个树突细胞的footprint。从小鼠骨髓中提取并培养经典的树突细胞1型(cDC1)和浆细胞样树突细胞 ...
比如下面的代码,使用JASPAR数据库中的motifs作为默认值进行motif匹配: $ rgt-motifanalysis matching--organism=mm9--input-files pDC.bed cDC1.bed>>output location:/media/yf/ATAC/Footprinting/hint/DendriticCells/match>>genome:mm9>>pseudocounts:1.0>>fpr threshold:0.0001>>>input file pDC loaded:312544regio...
J Granja et al., Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia. Nat Biotechnol. 37, 12 (2019). https://support.10xgenomics.com/single-cell-atac/software/visualization/latest/tutorial 关于10x Genomics ...
https://yiweiniu.github.io/blog/2019/03/ATAC-seq-data-analysis-from-FASTQ-to-peaks/A similar github page presenting an ATAC-seq pipeline https://galaxyproject.github.io/training-material/topics/epigenetics/tutorials/atac-seq/tutorial.html
Tutorial Three: In this section we will focus on differential peak identification, motif footprinting, and annotation of nearby genomic features. Workflow for sc-ATAC Sequencing (submodule 4). Tutorial Four: In this section we will demonstrate a single cell ATAC-Seq analysis workflow. GCP Architectu...
Bioconductor2016 Single-cell-RNA-sequencing workshop by Sandrine Dudoit lab- [R] - SCONE, clusterExperiment, and slingshot tutorial. BiomedCentral Single Cell Omics collectin- collection of papers describing techniques for single-cell analysis and protocols. ...
Seurat包学习笔记(一):Guided Clustering Tutorial Seurat包学习笔记(二):Integration and Label Transfer Seurat包学习笔记(三):Analysis of spatial datasets Seurat包学习笔记(四):Using sctransform in Seurat Seurat包学习笔记(五):Using Seurat with multi-modal data ...
J Granja et al., Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia. Nat Biotechnol. 37, 12 (2019). https://support.10xgenomics.com/single-cell-atac/software/visualization/latest/tutorial