Li Jiuxuan's repositories
ArchR_2020
Publication Page for ArchR Manuscript 2020
autoreg
A research compendium: Transcriptional regulation of autophagy during adipocyte differentiation
AuTToFlux
Pipeline for high-throughput analysis of RFP/GFP ratios in vacuoles
CellNet
CellNet: network biology applied to stem cell engineering
covid19
š¦ Regularly updated list of publicly available datasets with single-cell (scRNAseq) and T-cell/antibody immune repertoire (AIRR / RepSeq / immunosequencing) data of COVID-19 patients with SARS-CoV-2.
excelerate-scRNAseq
Single RNA-seq data analysis with R (Finland, May, 2019)
FCA_liver
All software used for āDecoding human fetal liver haematopoiesisā (Popescu, Botting, Stephenson et al., 2019).
HCA_Benchmarking
This repository contains HCA Benchmarking codes
masif
MaSIF- Molecular surface interaction fingerprints. Geometric deep learning to decipher patterns in molecular surfaces.
metaDEGth
metaDEGth: meta-analysis of Differentially Expressed Genes using parametric, empirically-derived P-value distributions
my-R
a small collection for my R scripts
R-Intro
Introduction to R - first steps: expressions, functions and data
rtfbs_db
Parse TF motifs from public databases, read into R, and scan using 'rtfbs'.
scfind-paper-figures
Scripts to recreate figures from the scfind paper
scRNA-tools
Table of software for the analysis of single-cell RNA-seq data.
scRNAseq-analysis-notes
scRNAseq analysis notes from Ming Tang
seurat
R toolkit for single cell genomics
simpleGO
Simple and fast GO enrichment tool with functional clustering
SingleR
SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
tabula-muris-senis
Tabula Muris Senis
Targeted_transcriptomics
Mair and Erickson, A targeted multi-omic analysis approach measures protein expression and low abundance transcripts on the single cell level
TFbenchmark
This repository contains the code used to benchmark TF-target datasets via TF activities in 3 benchmark datasets
TFBSTools
Software Package for Transcription Factor Binding Site (TFBS) Analysis
TFpredict
Identification and structural characterization of transcription factors based on supervised machine learning