MattPM

guiltytargets

Target prioritization using network representation learning

utility

Collection of Tumor-Infiltrating Lymphocyte Single-Cell Experiments with TCR

awesome-causality-algorithms

An index of algorithms for learning causality with data

scglmmr

Sample-level Single-cell Generalized Linear Multilevel Models in R

macos-auto-clicker

A simple auto clicker for macOS Big Sur, Monterey, Ventura and Sonoma.

LCV

Software implementing the Latent Causal Variable Model

zenodo-docs-user

Zenodo User Documentation

tuning_playbook

A playbook for systematically maximizing the performance of deep learning models.

lme4

Mixed-effects models in R using S4 classes and methods with RcppEigen

drug_targeting

presto

Fast Wilcoxon and auROC

HDStIM

HDStIM: High Dimensional Stimulation Immune Mapping

dsb

Normalize CITEseq Data

RNA-seq-analysis

RNAseq analysis notes from Ming Tang

qsmooth

Smooth quantile normalization (qsmooth) is a generalization of quantile normalization, which is an average of the two types of assumptions about the data generation process: quantile normalization and quantile normalization between groups.

APM_Exercises

Exercises for the book Applied Predictive Modeling by Kuhn and Johnson (2013)

StatisticalRethinking.jl

Julia package with selected functions in the R package `rethinking`. Used in the SR2... projects.

CITE-sort

stat_rethinking_2022

Statistical Rethinking course winter 2022

lecture_notes

Lecture Notes on Computational and Mathematical Population Genetics

LinearMixedEffectsModels

ezDAFi

Easy-to-use Directed Automated Filtering and Identification of cell populations in single cell data

GaussianMixtures.jl

Large scale Gaussian Mixture Models

TumorShallowSeq

Cancer prognosis with shallow tumor RNA sequencing

SIGNAL

TRIAGE (Throughput Ranking by Iterative Analysis of Genomic Enrichment)

variancePartition

Quantify and interpret divers of variation in multilevel gene expression experiments

statrethinking_winter2019

Statistical Rethinking course at MPI-EVA from Dec 2018 through Feb 2019

scRepertoire

A toolkit for single-cell immune profiling

SingleCellThoughts

Assorted thoughts, explanations and justifications for code in the scran package and the simpleSingleCell workflow.

demuxlet

Genetic multiplexing of barcoded single cell RNA-seq