agitter
Associate professor in Biostatistics and Medical Informatics at the University of Wisconsin-Madison; Investigator at the Morgridge Institute for Research
Pinned Repositories
lightchem
Light-weight Machine Learning Framework for Drug Discovery
manubot-awesome-list
Proof of concept for creating awesome lists with Manubot
py-upset
A pure-python implementation of the UpSet suite of visualisation methods by Lex, Gehlenborg et al.
sdrem
Signaling and Dynamic Regulatory Events Miner
single-cell-pseudotime
An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
metl
Mutational Effect Transfer Learning (METL) framework for pretraining and finetuning biophysics-informed protein language models
nn4dms
Neural networks for deep mutational scanning data
ssps
Sparse Signaling Pathway Sampling: MCMC for signaling pathway inference
rootstock
Clone me to create your Manubot manuscript
spras
Signaling Pathway Reconstruction Analysis Streamliner (SPRAS)
agitter's Repositories
agitter/single-cell-pseudotime
An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
agitter/manubot-awesome-list
Proof of concept for creating awesome lists with Manubot
agitter/my-manuscript
Test manuscript from https://github.com/manubot/rootstock
agitter/Awesome-Biomolecule-Language-Cross-Modeling
Awesome-Biomolecule-Language-Cross-Modeling: a curated list of resources for paper "Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Survey"
agitter/deep-review
A collaboratively written review paper on deep learning, genomics, and precision medicine
agitter/dmol-book
Deep learning for molecules and materials book
agitter/Machine-learning-for-proteins
Listing of papers about machine learning for proteins.
agitter/ProteinDT
agitter/proteomics-tutorial
agitter/rosetta
The Rosetta Bio-macromolecule modeling package.
agitter/awesome-self-driving-labs
A curated list of self-driving laboratories that combine hardware automation and artificial intelligence to accelerate scientific discovery.
agitter/chtc-website-source
Source markdown and contents of the CHTC website
agitter/compbio-edi
Curated summary of efforts to promote equity, diversity, and inclusion in computational biology PhD programs and societies.
agitter/covid19-review
A collaborative review of the emerging literature on diagnostics and treatments related to COVID-19
agitter/deep-rules
Ten Simple Rules for Deep Learning in Biology
agitter/folding_tools
A collection of *fold* tools
agitter/hpc-python
HPC Python lesson materials
agitter/htcondor
Snakemake profile for HTCondor
agitter/manubot
The manuscript bot for automated scholarly publishing (Python package)
agitter/manufesto
Manubot manifesto
agitter/ml4bio-workshop
Materials for a workshop introducing machine learning to biologists
agitter/OmicsIntegrator2
Prize-Collecting Steiner Forests for Interactomes
agitter/PathLinker
Connect the dots in networks.
agitter/sanbomics
bioinformatics plotting and tools
agitter/scikit-learn
scikit-learn: machine learning in Python
agitter/SCODE
SCODE : an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation
agitter/snakemake-demos
Example Snakefiles for various use cases
agitter/spras
Signaling Pathway Reconstruction Analysis Streamliner (SPRAS)
agitter/templates-GPUs
Template job submissions using GPUs in CHTC
agitter/try-manubot
A repository to practice contributing to a Manubot manuscript