Pinned Repositories
Adult_brain_somatic_mosaicism
This repository collects pipelines, codes, and some intermediate results for adult brain somatic mosaicism study.
ATAC-seq
awesome-single-cell
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
awesome_spatial_omics
tools and notes for spatial omics
BrCa_cell_atlas
Data processing and analysis related code associated with the study "A single-cell and spatially resolved atlas of human breast cancers".
GENESPACE
GeneTrajectory
R implementation of GeneTrajectory
igv_utils
utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.
lapa
Alternative polyadenylation detection from diverse data sources such as 3'-seq, long-read and short-reads.
PigGTEx-Pipeline-v0
lipingshu's Repositories
lipingshu/GENESPACE
lipingshu/GeneTrajectory
R implementation of GeneTrajectory
lipingshu/PigGTEx-Pipeline-v0
lipingshu/awesome-single-cell
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
lipingshu/awesome_spatial_omics
tools and notes for spatial omics
lipingshu/CellphoneDB
CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
lipingshu/cellrank
CellRank: dynamics from multi-view single-cell data
lipingshu/clusterProfiler_protocol
omics data analysis using clusterProfiler ;)
lipingshu/DoubletFinder
R package for detecting doublets in single-cell RNA sequencing data
lipingshu/dx-toolkit
DNAnexus platform client libraries
lipingshu/GPTCelltype
lipingshu/hifiasm
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
lipingshu/juicer
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
lipingshu/monocle3
lipingshu/omicverse
A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
lipingshu/Pan_Ath
Code for Article "A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range"
lipingshu/panpipes
Multi-modal single cell analysis pipelines
lipingshu/panpipes-tutorials
tutorials to run panpipes
lipingshu/PINNACLE
Contextualizing protein representations using deep learning on protein networks and single-cell data
lipingshu/PRIDICT2
lipingshu/quantms
Quantitative mass spectrometry workflow.
lipingshu/scanpy
Single-cell analysis in Python. Scales to >1M cells.
lipingshu/scRNAseq-analysis-notes
scRNAseq analysis notes from Ming Tang
lipingshu/Single-cell-atlas-of-the-human-brain-vasculature-accross-development-adulthood-and-disease
Molecular atlas of the human brain vasculature accross development, adulthood and disease at the single-cell level
lipingshu/snipit
snipit: summarise snps relative to your reference sequence
lipingshu/spatial-lung-fibrosis
Repository for all R scripts used for the bioinformatic analyses of the mouse and human 10x Genomics Visium spatially resolved transcriptomics data presented in our associated manuscript.
lipingshu/SpatialGlue
SpatialGlue is a novel deep learning methods for spatial multi-omics data integration.
lipingshu/trackViewer
A bioconductor package with minimalist design for drawing elegant tracks or lollipop plot
lipingshu/tutorial-template
Template for the Read the Docs tutorial
lipingshu/UKB_RAP
Access share reviewed code & Jupyter Notebooks for use on the UK Biobank (UKBB) Research Application Platform. Includes resources from DNAnexus webinars, online trainings and workshops.