tools and notes for spatial omics

Bootstrap for Rapid Inference on Spatial Covariances

Comprehensive list of color palettes available in R ❤️🧡💛💚💙💜

Contains files for the deep learning in genomics primer.

Uniform Manifold Approximation and Projection

This Snakemake pipeline implements the GATK best-practices workflow

An R Interface to the ImmuneSpace database portal

R wrapper around the ImmPort API and its download tool

Uniform Manifold Approximation and Projection - R package

Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets

R package to estimate q-values and false discovery rate quantities.

Some Examples for Rcpp Workshop

Functions for identifying and characterizing continuous developmental trajectories in single-cell data.

Collection of jupyter notebooks for demonstrating software.

More robust R programming, testing and debugging

Data science Python notebooks: Deep learning (TensorFlow, Theano, Caffe, Keras), scikit-learn, Kaggle, big data (Spark, Hadoop MapReduce, HDFS), matplotlib, pandas, NumPy, SciPy, Python essentials,…

Tools for bioinformatics moved to http://git.genenetwork.org/pjotrp/bioinformatics

Talk at Workshop on Visualization for Big Data: Strategies and Principles, Fields Institute http://www.fields.utoronto.ca/programs/scientific/14-15/bigdata/visualization/

The Leek group guide to genomics papers

R boot-camp

Various teaching material