lipingshu's repositories
GeneTrajectory
R implementation of GeneTrajectory
awesome_spatial_omics
tools and notes for spatial omics
ChatGPT
Lightweight package for interacting with ChatGPT's API by OpenAI. Uses reverse engineered official API.
FastGithub
github加速神器，解决github打不开、用户头像无法加载、releases无法上传下载、git-clone、git-pull、git-push失败等问题
ffq
A tool to find sequencing data and metadata from public databases.
gget
🧬 gget enables efficient querying of genomic reference databases
GSEApy
Gene Set Enrichment Analysis in Python
DoubletFinder
R package for detecting doublets in single-cell RNA sequencing data
GenoVi
GenoVi, an automated customizable circular genome visualizer for bacteria and archaea
hifiasm
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
kallisto
Near-optimal RNA-Seq quantification
long-read-pipelines
Long read production pipelines
MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
NGenomeSyn
Any Way to Show Multi genomic Synteny
Pan_Ath
Code for Article "A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range"
Pervasive_positive_selection_in_blood
Code accompanying the manuscript 'Pervasive positive selection in blood in 200,618 individuals and novel drivers of clonal haematopoiesis'.
PyWGCNA
PyWGCNA is a Python package designed to do Weighted correlation network analysis (WGCNA)
scanpy
Single-cell analysis in Python. Scales to >1M cells.
scGCL
scGCL: an imputation method for scRNA-seq data based on Graph Contrastive Learning
scRNAseq-analysis-notes
scRNAseq analysis notes from Ming Tang
segment-anything
The repository provides code for running inference with the SegmentAnything Model (SAM), links for downloading the trained model checkpoints, and example notebooks that show how to use the model.
seurat
R toolkit for single cell genomics
shapeit4
Segmented HAPlotype Estimation and Imputation Tool
swan_vis
A Python library to visualize and analyze long-read transcriptomes