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2020_wilk_covid

Reproducibility repository accompanying Wilk, Rustagi, Zhao, et al. "A single-cell atlas of the peripheral immune response to severe COVID-19"

amlhierarchies

Analysis notebooks and data for AML hierarchies paper

complexheatmap

Make Complex Heatmaps

cuimc-nyp_covid_autopsy_lung

datasetdownloader

devtum

Developmental Deconvolution for Classification of Cancer Origin

faers-data-toolkit

Script tools for downloading, data preprocessing, data merging and standardizing for FDA Adverse Event Reporting System(FAERS) dataset.

metaicb

netbio

omivae

End-to-end deep learning model for low dimensional latent space extraction and multi-class classification on multi-omics datasets.

pancaf

pisces

R package for Protein activity analysis of single-cell RNAseq.

sanbomics_scripts

scripts and notebooks from sanbomics

scavenge

SCAVENGE is a method to optimize the inference of functional and genetic associations to specific cells at single-cell resolution.

scgpt

sclc-cancer-cell-manuscript

SCLC--Cancer-Cell-bulk RNA and sc-RNA public datasets

scrnatoolvis

Useful functions to make your scRNA-seq plot more cool!

single-cell-rcc-pipeline

Data files and code for analysis of single-cell ccRCC data for the manuscript "Tumor-Specific Cell Populations in Clear Cell Renal Carcinoma Associated with Clinical Outcome Identified Using Single-Cell Protein Activity Inference." Includes code for VIPER protein activity inference pipeline

singlecells_sle_pbmcpaper

Scripts used for the analysis of single cell SLE PBMCs

tg-gates

Import and analysis of TG-GATES data for machine learning pipeline.

tip

TIP: Tri-graph Interaction Propagation model for Polypharmacy Side Effect Prediction (GRL@NeurIPS, 2019)

velocyto.py

RNA velocity estimation in Python

velocyto.r

RNA velocity estimation in R on Windows 10/11

zhang-zeming-20221109nature

Codes for the scPLC project