Ruben Dries's repositories
Giotto_site
Website for the Giotto spatial toolbox
fluidSCqpcr
R package to pre-process, analyze and visualize single-cell qPCR data
Giotto_site_dev
Giotto documentation for development version
bioc-refcard
Bioconductor cheat sheet
GiottoData
Spatial datasets and helper functions to test and work with Giotto Suite
long-rna-seq-pipeline
STAR based ENCODE Long RNA-Seq processing pipeline
Rfast
A collection of Rfast functions for data analysis. Note 1: The vast majority of the functions accept matrices only, not data.frames. Note 2: Do not have matrices or vectors with have missing data (i.e NAs). We do no check about them and C++ internally transforms them into zeros (0), so you may get wrong results. Note 3: In general, make sure you give the correct input, in order to get the correct output. We do no checks and this is one of the many reasons we are fast.
RNAseq_pipeline
An easy and simple RNAseq pipeline for the first step of processing raw fastq files.
spatialexperiment-analysis
repo to explore spatial data in R/Bioconductor and Python
vitessceR
R API and htmlwidget for Vitessce
whitePaper
Manubot for white paper