Zewen Kelvin Tuong's repositories
databases_for_vdj
databases for V(D)J-seq
dandelion-demo-files
demo files for sc-dandelion and notebooks accompanying dandelion manuscript
cardelino
Clone identification from single-cell data
CellphoneDB
CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
ClonalOmics
Python notebooks containing analysis of clonal gene expression, with a bit of proteomics and ATAC for good measure.
ecosystem-packages
Registry for scverse ecosystem packages
Genes2Genes
Aligning transcriptomic trajectories of single-cell reference and query systems
mgatk
mgatk: mitochondrial genome analysis toolkit
milopy
Python implementation of Milo for differential abundance testing on KNN graph
nextNEOpi
nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
Palantir
Single cell trajectory detection
pybliometrics
Python-based API-Wrapper to access Scopus
pyCirclize
Circular visualization in Python (Circos Plot, Chord Diagram)
PyDESeq2
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
pyslingshot
Python implementation of the Slingshot pseudotime algorithm
receptor_utils
Misc utilities for receptor gene sequences
scirpy
A scanpy extension to analyse single-cell TCR and BCR data.
single-cell-best-practices
https://www.sc-best-practices.org
tcrdist3
flexible CDR based distance metrics
troubleshooting_palantir
just to hold some notebooks as i troubleshoot palantir
variancePartition
Quantify and interpret divers of variation in multilevel gene expression experiments
VIA
trajectory inference