top of page
Zhisong Jeff HE
何志嵩
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
-
Bardy et al. 2016: Download from Google Drive
-
Close et al. 2017: Download from Google Drive
-
Darmanis et al. 2015: Download from Google Drive
-
Lake et al. 2016: Download from Google Drive​
Mouse Datasets
-
Chen et al. 2017: Download from Google Drive
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
bottom of page