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BIOINFORMATICS TOOLS
  • Pando: An R package to infer GRN given single-cell multiomic (RNA+ATAC) data, combining TFBS prediction and (regularized) linear regression model.
  • simspec: An R package to calculate Reference/Cluster Similarity Spectrum (RSS/CSS) representation of single-cell RNA-seq data
  • HiTSeq: A JAVA tool for RNA-seq read counting and intron-centric alternative splicing event construction
DATA PORTALS
  • scApeX: The Shiny app visualizing the scRNA-seq/ATAC-seq data presented in the Kanton et al. 2019 Nature paper (human/chimp/macaque cerebral organoid and adult cortical layers)
External data used in "Identification and characterization of functional modules reflecting transcriptome transition during human neuron maturation"

Human Datasets

Mouse Datasets

Usage:

Load the downloaded file in R. For each data set, the loaded list object contains three components:

  • fpkm: The FPKM table of genes in samples of the data set

  • info: The sample information table

  • fpkmStd: The  table of standardized expression of selected marker genes for NMI models

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