beyondpie / CEMBA_wmb_snATAC

Whole mouse brain snATAC seq analysis
MIT License
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[[./repo_figures/GraphAbstract.jpg]]

** Data

** Pipeline

[[./repo_figures/snATAC-seq_analysis_pipeline.jpg]]
Codes ** Clustering In total, we have implemented four-round iterative clustering. See details in [[file:01.clustering][01.clustering]] Integration and annotation We use Allen's scRNAseq data and their annotations for our data annotation. See details in [[file:02.integration][02.integration]] Peak calling We use macs2 with multiple stage filtering, especially use SPM >= 5 for filtering peaks. See details in [[file:03.peakcalling][03.peakcalling]] Comments on some scripts:

  1. [[file:package/R/cembav2env.R][cembav2env.R]]: R env to store the metadata during analysis. |----------------+-------------------------------------------------------| | Enviorment | Description | |----------------+-------------------------------------------------------| | cembav2env | meta data of SnapATAC and SnapATAC2 | |----------------+-------------------------------------------------------| | cluSumBySa2 | clustering meta data, such as resolution, | | | barcode to L4 Ids, L4 major regions and so on | |----------------+-------------------------------------------------------| | Sa2Integration | Integration meta data, like Allen's data descriptions | |----------------+-------------------------------------------------------| | Sa2PeakCalling | Peak calling meta data | |----------------+-------------------------------------------------------|