This repository include the following pipelines for scRNAseq data analysis
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dronc: analyze single-nucleus RNA-seq data from human brain generated by DroNc-seq pipeline.
Habib, Naomi, et al. "Massively parallel single-nucleus RNA-seq with DroNc-seq." Nature methods 14.10 (2017): 955.
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MTG: analyze single-nucleus RNA-seq data from human brain Allen Brain Atlas MTG (Middle Temporal Gyrus) dataset.
http://celltypes.brain-map.org/rnaseq. ``In total, 15,928 nuclei from 8 human tissue donors ranging in age from 24-66 years were analyzed. Analysis of these transcriptional profiles reveals approximately 75 transcriptionally distinct cell types, subdivided into 45 inhibitory neuron types, 24 excitatory neuron types, and 6 non-neuronal types.''
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PBMC_68k: a general purpose pipeline using PBMC 68k data (10x Genomics, Zheng et al. 2017) as an demonstration.
Zheng, Grace XY, et al. "Massively parallel digital transcriptional profiling of single cells." Nature communications 8 (2017): 14049.
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psychENCODE: analyze single-nucleus RNA-seq data from psychENCODE project as well as a few existing studies.
Wang, Daifeng, et al. "Comprehensive functional genomic resource and integrative model for the human brain." Science 362.6420 (2018): eaat8464.