Davis Laboratory
Computational systems oncology lab at the South Australian Immunogenomics Cancer Institute (SAiGENCI)
Australia
Pinned Repositories
dcanr
Differential co-expression/association network analysis
GeoMXAnalysisWorkflow
GeoMX analysis workflow
hoodscanR
msImpute
Methods for label-free mass spectrometry proteomics
NK_scoring
PySingscore
scDECAF
Reference-free celltype and phenotype annotation in single cell RNAseq by learning geneset representations
singscore
An R/Bioconductor package that implements a single-sample molecular phenotyping approach
standR
Spatial transcriptomics analyses and decoding in R
vissE
An R/Bioconductor package to identify higher-order molecular phenotypes
Davis Laboratory's Repositories
DavisLaboratory/singscore
An R/Bioconductor package that implements a single-sample molecular phenotyping approach
DavisLaboratory/standR
Spatial transcriptomics analyses and decoding in R
DavisLaboratory/msImpute
Methods for label-free mass spectrometry proteomics
DavisLaboratory/vissE
An R/Bioconductor package to identify higher-order molecular phenotypes
DavisLaboratory/scDECAF
Reference-free celltype and phenotype annotation in single cell RNAseq by learning geneset representations
DavisLaboratory/dcanr
Differential co-expression/association network analysis
DavisLaboratory/GeoMXAnalysisWorkflow
GeoMX analysis workflow
DavisLaboratory/hoodscanR
DavisLaboratory/mastR
An R package for automatically screening cell type signature in specific tissue/organ/cancer.
DavisLaboratory/emtdata
DavisLaboratory/GenesetAnalysisWorkflow
DavisLaboratory/msigdb
A R/Bioconductor ExperimentHub package to access gene expression signatures in the Molecular Signatures Database (MSigDB).
DavisLaboratory/Db_Compare
Compares the databases Reactome, KEGG, HPRD, WikiPathways and PhosphoSitePlus on their coverage of phospho/proteomic data.
DavisLaboratory/Jacquelot_2021_reproducibility
Source code and application note for ILC2 classifier developed in Jacquelot et al., 2021
DavisLaboratory/peptide-protonet
Embedding MS1 peptide features and identification transfer
DavisLaboratory/peptideprotonet_reproducibility
Scripts and notebooks to reproduce figures for the peptideprotonet manuscript
DavisLaboratory/SingscoreAMLMutations
DavisLaboratory/smartid
An R package for Scoring and Marker Selection Based on Modified TF-IDF
DavisLaboratory/SubcellularSpatialData
This repository hosts a data package with annotated sub-cellular resolution spatial transcriptomics datasets.
DavisLaboratory/maph
a command line tool for analysing phosphoproteomics data
DavisLaboratory/msImpute-reproducibility
Code to reproduce figures in msImpute manuscript and tutorials
DavisLaboratory/nf_modules
Modules for scripting with nextflow
DavisLaboratory/scDECAF-reproducibility
Code to reproduce figures for scDECAF manuscript
DavisLaboratory/BiocStickers
Stickers for some Bioconductor packages - feel free to contribute and/or modify.
DavisLaboratory/mforoutan_tgfb_2017_celllines
This repository contains Dockerfile for the following paper: A Transcriptional Signature for TGFβ-induced EMT in Cancer (cell-line analysis)
DavisLaboratory/mforoutan_tgfb_2017_tumours
This repository contains Dockerfile for the following paper: A Transcriptional Signature for TGFβ-induced EMT in Cancer - Tumour analysis
DavisLaboratory/mforoutan_tgfb_paper_2016
Docker file for TGFb paper
DavisLaboratory/MultipleExperiment
DavisLaboratory/SanJuan_etal_reproducibility
Code to reproduce the results for San Juan et al. 2022
DavisLaboratory/SpatialLibrarySizePaper