Pinned Repositories
ACTION
Archetypal analysis for Cell Type identificatION (ACTION)
Anchor
This is the package of Yuanfang's winning algorithm in the ENCODE-DREAM in vivo Transcription Factor Binding Site Prediction Challenge
germcell
Single-cell RNA-seq analysis of human germline cells and their niche cells
germcellshiny
Shiny of Gem Cell Expression
HECA
Human embryonic cell altas
RSCORE
scRNAseq_workflow_benchmark
Workflow for the analysis fo single-cell RNASeq data using R/bioconductor
Texomer
Texomer: Integrating Analysis of Cancer Genome and Transcriptome Sequencing Data
zorrodong.online
Zorro's Homepage
zorrodong's Repositories
zorrodong/HECA
Human embryonic cell altas
zorrodong/zorrodong.online
Zorro's Homepage
zorrodong/Bat-Cochlea
Study the molecular mechanism of mammalian hearing frequency variation
zorrodong/cellassign
Automated, probabilistic assignment of cell types in scRNA-seq data
zorrodong/chisel
CHISEL -- Copy-number Haplotype Inference in Single-cell by Evolutionary Links
zorrodong/DoubletFinder
R package for detecting doublets in single-cell RNA sequencing data
zorrodong/dropSeqPipe
A SingleCell RNASeq pre-processing snakemake workflow
zorrodong/epiConv
single-cell ATAC-seq data analysis
zorrodong/gffutils
GFF and GTF file manipulation and interconversion
zorrodong/Giotto
Single-cell spatial analysis pipeline
zorrodong/GMM-Demux
zorrodong/HLCA
zorrodong/homologene
:mouse: :left_right_arrow: :couple: An r package that works as a wrapper to homologene
zorrodong/MAESTRO
Single-cell Transcriptome and Regulome Analysis Pipeline
zorrodong/MOFA2
Multi-Omics Factor Analysis V2 (MOFA+)
zorrodong/mosdepth
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
zorrodong/muscat
Multi-sample multi-group scRNA-seq analysis tools
zorrodong/nichenetr
NicheNet: predict active ligand-target links between interacting cells
zorrodong/PoincareMaps
The need to understand cell developmental processes has spawned a plethora of computational methods for discovering hierarchies from scRNAseq data. However, existing techniques are based on Euclidean geometry which is not an optimal choice for modeling complex cell trajectories with multiple branches. To overcome this fundamental representation issue we propose Poincaré maps, a method harnessing the power of hyperbolic geometry into the realm of single-cell data analysis.
zorrodong/scarches
architecture surgery and transfer learning for single-cell
zorrodong/scATAC-pro
A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
zorrodong/scDblFinder
Methods for detecting doublets in single-cell RNAseq data
zorrodong/SCENICprotocol
A scalable SCENIC workflow for single-cell gene regulatory network analysis
zorrodong/scrnaseq
A single-cell RNAseq pipeline for 10X genomics data
zorrodong/scRNAseq_pipelines
zorrodong/simspec
Calculation of Reference/Cluster Similarity Spectrum (RSS/CSS)
zorrodong/snRNA-seq2_young
Analysis of snRNA-seq2 data coming from 3 months old mouse liver, dissecting the influence ploidy has on gene expression.
zorrodong/souporcell
Clustering scRNAseq by genotypes
zorrodong/template
A template Sphinx repo
zorrodong/UPhyloplot2
Draw phylogenetic trees of tumor evolution