Projects in Awesome Lists by FertigLab
A curated list of projects in awesome lists by FertigLab .
https://github.com/fertiglab/cancerinsilico
An R package for running cell-based models
bioconductor cell-based monte-carlo off-lattice-model rcpp
Last synced: 17 Jan 2026
https://github.com/fertiglab/geneoscollaboration
Repository for R code for single cell sequencing analysis published in Yarchoan, M., Gane, E.J., Marron, T.U. et al. Personalized neoantigen vaccine and pembrolizumab in advanced hepatocellular carcinoma: a phase 1/2 trial. Nat Med (2024).
Last synced: 17 Jan 2026
https://github.com/fertiglab/singlecelltimecourse
Head and neck cancer rna velocity scripts
Last synced: 17 Jan 2026
https://github.com/fertiglab/seva
Code for analyses in Splice Expression Variation Analysis (SEVA) for Inter-tumor Heterogeneity of Gene Isoform Usage in Cancer
Last synced: 17 Jan 2026
https://github.com/fertiglab/projectrspatialexample
Application of projectR for spatial analysis
Last synced: 17 Jan 2026
https://github.com/fertiglab/cogapsdocker
Docker container for running cogaps
Last synced: 17 Jan 2026
https://github.com/fertiglab/jhpce_scripts_for_cogaps
Template scripts for running CoGAPS on JHPCE
Last synced: 17 Jan 2026
https://github.com/fertiglab/clutrfree
C++ implementation of ClutrFree package
Last synced: 17 Jan 2026
https://github.com/fertiglab/emt_ewald
Curated set of analysis scripts for single cell data from the Ewald Lab.
Last synced: 17 Jan 2026
https://github.com/fertiglab/cogapscli
Standalone Command Line Version of CoGAPS
Last synced: 17 Jan 2026
https://github.com/fertiglab/pdac_atlas
Analysis workflow for all data present in our PDAC Atlas Manuscript titled, "Transfer learning associates CAFs with EMT and inflammation in tumor cells in human tumors and organoid co-culture in pancreatic ductal adenocarcinoma"
Last synced: 17 Jan 2026
https://github.com/fertiglab/pycogaps-gpn
PyCoGAPS for support with GenePattern Notebook.
Last synced: 17 Jan 2026
https://github.com/fertiglab/cellsinspace
using spatial transcriptomics to inform a model of hypoxia in tumor cells.
Last synced: 17 Jan 2026
https://github.com/fertiglab/j1798_trial_paper
scripts for the J1798 trial paper
Last synced: 17 Jan 2026
https://github.com/fertiglab/mkras-vax
scRNA and TCR analysis, including T-cell expansion assays, from subjects in J1994 manuscript by Huff et al.
Last synced: 17 Jan 2026
https://github.com/fertiglab/hpv2013analysis
Scripts to replicate the analysis from Fertig et al. (2013) https://doi.org/10.1371/journal.pone.0078127
Last synced: 17 Jan 2026
https://github.com/fertiglab/pacvax2_pancvaxici_scrnaseq
scRNAseq and survival analysis in Panc02-bearing mice treated with PancVAX and immune checkpoint inhibition
Last synced: 17 Jan 2026
https://github.com/fertiglab/cogapsdevtools
Tools useful for developers of CoGAPS
Last synced: 16 Jan 2026
https://github.com/fertiglab/cogaps-bioc
This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/CoGAPS.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=CoGAPS.
Last synced: 17 Jan 2026
https://github.com/fertiglab/j1568_bulk
Repository created to house code pertaining to the J1568 MultiOmics Paper
Last synced: 17 Jan 2026
https://github.com/fertiglab/vb
Variational Approximation implementation of CoGAPS
Last synced: 17 Jan 2026
https://github.com/fertiglab/splicemutr_paper
Generating the figures from supplementary data for the splicemutr paper
Last synced: 17 Jan 2026