zktuong
I'm a Group leader at The University of Queensland on Pediatric Systems Immunology and I use R and python to analyse lots of single-cell RNAseq data
The University of Queensland
Pinned Repositories
dandelion
dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data
databases_for_vdj
databases for V(D)J-seq
getSRA
wrapper bash scripts to download fastq files from SRR
kelvinny
Kelvin's R package that holds wrapper functions for a number of work things
ktplots
Some tools for plotting single-cell data
ktplotspy
Python library for plotting Cellphonedb results. Ported from ktplots R package.
scFunctions
Functions for single cell data analysis
zktuong's Repositories
zktuong/ktplots
Some tools for plotting single-cell data
zktuong/dandelion
dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data
zktuong/ktplotspy
Python library for plotting Cellphonedb results. Ported from ktplots R package.
zktuong/databases_for_vdj
databases for V(D)J-seq
zktuong/getSRA
wrapper bash scripts to download fastq files from SRR
zktuong/asi_sig_hackathon
My notebooks to test some tools
zktuong/cardelino
Clone identification from single-cell data
zktuong/CellphoneDB
CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
zktuong/cellphonedb-data
zktuong/ClonalOmics
Python notebooks containing analysis of clonal gene expression, with a bit of proteomics and ATAC for good measure.
zktuong/CMapForDC
zktuong/dandelion-demo-files
demo files for sc-dandelion and notebooks accompanying dandelion manuscript
zktuong/ecosystem-packages
Registry for scverse ecosystem packages
zktuong/Genes2Genes
Aligning transcriptomic trajectories of single-cell reference and query systems
zktuong/mgatk
mgatk: mitochondrial genome analysis toolkit
zktuong/milopy
Python implementation of Milo for differential abundance testing on KNN graph
zktuong/nextNEOpi
nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
zktuong/Palantir
Single cell trajectory detection
zktuong/pybliometrics
Python-based API-Wrapper to access Scopus
zktuong/pyCirclize
Circular visualization in Python (Circos Plot, Chord Diagram)
zktuong/PyDESeq2
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
zktuong/pyslingshot
Python implementation of the Slingshot pseudotime algorithm
zktuong/receptor_utils
Misc utilities for receptor gene sequences
zktuong/scirpy
A scanpy extension to analyse single-cell TCR and BCR data.
zktuong/single-cell-best-practices
https://www.sc-best-practices.org
zktuong/tcrdist3
flexible CDR based distance metrics
zktuong/troubleshooting_palantir
just to hold some notebooks as i troubleshoot palantir
zktuong/ulipstic-analysis
zktuong/variancePartition
Quantify and interpret divers of variation in multilevel gene expression experiments
zktuong/VIA
trajectory inference