slagtermaarten
PhD student working on computational/bioinformatics problems in tumor immunology at the Schumacher and Wessels labs, Netherlands Cancer Institute
Amsterdam, the Netherlands
Pinned Repositories
cyto_inference
Analyses for a manuscript by Hoekstra & Slagter et al. involving the use of transcriptomic read-outs to infer the spreading of cytokines through the tumor microenvironment
DISTINCT
Probabilistic label transfer from bulk to single cell RNASeq datasets using TRANSACT data integration
dotfiles
Fork and edit from thoughtbot/dotfiles
genesets
A repo of genesets and R functionality to read them
hashtagassignment
knitr
A general-purpose tool for dynamic report generation in R
LOHHLA
Fork of https://bitbucket.org/mcgranahanlab/lohhla
maartenutils
General utilities for R development
quickMHC
Cache and lookup antigen predictions
TONIC
Analyses for the TONIC trial lead by Marleen Kok at the Netherlands Cancer Institute
slagtermaarten's Repositories
slagtermaarten/LOHHLA
Fork of https://bitbucket.org/mcgranahanlab/lohhla
slagtermaarten/DISTINCT
Probabilistic label transfer from bulk to single cell RNASeq datasets using TRANSACT data integration
slagtermaarten/cyto_inference
Analyses for a manuscript by Hoekstra & Slagter et al. involving the use of transcriptomic read-outs to infer the spreading of cytokines through the tumor microenvironment
slagtermaarten/dotfiles
Fork and edit from thoughtbot/dotfiles
slagtermaarten/genesets
A repo of genesets and R functionality to read them
slagtermaarten/maartenutils
General utilities for R development
slagtermaarten/TONIC
Analyses for the TONIC trial lead by Marleen Kok at the Netherlands Cancer Institute
slagtermaarten/bulk_velo-nf
Expression velocity to bulk data
slagtermaarten/hashtagassignment
slagtermaarten/quickMHC
Cache and lookup antigen predictions
slagtermaarten/ALICE
Detecting TCR involved in immune responses from single RepSeq datasets
slagtermaarten/antigen.garnish
slagtermaarten/cacheR
Make a function cache its result such that any combination of arguments will only need to be evaluated once
slagtermaarten/cc3d_build_scripts
build scripts for CC3D - used to automatize CC3D buids
slagtermaarten/ComplexHeatmap
Make Complex Heatmaps
slagtermaarten/CompuCell3D
CompuCell3D public source code repository
slagtermaarten/downsample-nf
Script for downsampling BAM files
slagtermaarten/firehosedownload
slagtermaarten/focus.vim
A Vim plugin that removes clutter and makes working on a widescreen monitor enjoyable.
slagtermaarten/immunoediting
Code associated with my immunoediting related work
slagtermaarten/init.lua
slagtermaarten/ipython
Official IPython repository
slagtermaarten/kknn
Weighted k-Nearest Neighbors
slagtermaarten/nvim-ide
Docker images that encapsulate a Linux machine running Neovim
slagtermaarten/serializer
Wrapper around existing serialization infrastructure in R (writeRDS) that obviates typical associated boilerplate code
slagtermaarten/slagtermaarten
Config files for my GitHub profile.
slagtermaarten/slagtermaarten.github.io
A beautiful, simple, clean, and responsive Jekyll theme for academics
slagtermaarten/slimux
SLIME inspired tmux integration plugin for Vim
slagtermaarten/snakemake-exome
Snakemake workflow for processing exome data.
slagtermaarten/TRANSACT
Python implementation of TRANSACT, a tool to transfer non-linear predictors of drug response from model systems to tumors.