R packages

Name Author(s) Description
aroma.affymetrix Henrik Bengtsson
James Bullard
Kasper Hansen
Pierre Neuvial
Elizabeth Purdom
Mark D Robinson
Ken Simpson
An open-source R framework for microarray analysis
BANDITS Simone Tiberi
Mark D Robinson
A Bayesian hierarchical model for differential splicing, via differential transcript usage, accounting for sample-to-sample variability and mapping uncertainty
CATALYST Helena L Crowell
Mark D Robinson
Vito RT Zanotelli
Stéphane Chevrier
Bernd Bodenmiller
Pipeline for preprocessing of cytometry data
& visualization tools for differential analysis
CellMixS Almut Lütge
Mark D Robinson
Toolbox to evaluate Cellspecific Mixing Scores (CMS) for different batches in scRNA-seq data
censcyt Reto Gerber censored covariates in differential abundance analysis in cytometry
countsimQC Charlotte Soneson Comparison of characteristic features of count data sets
CrispRVariants Helen Lindsay Tools for counting and visualising mutations in a target location
cytofWorkflow Malgorzata Nowicka CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets
DAMEfinder Stephany Orjuela
Dania Machlab
Mark D Robinson
Method to detect differential allele-specific methylation
DESpace Peiying Cai
Simone Tiberi
Mark D Robinson
A framework to discover spatially variable genes via spatial clusters
diffcyt Lukas M Weber Statistical methods for differential discovery in high-dimensional cytometry data
diffUTR Stefan Gerber
Pierre-Luc Germain
Streamlining differential exon and UTR usage analysis
distinct Simone Tiberi
Mark D Robinson
A statistical method to perform differential analyses between groups of distributions, ideal for applications to high-throughput single-cell data. By comparing full distributions, distinct identifies both, differential patterns involving changes in the mean, as well as more subtle variations that do not involve the mean.
DRIMSeq Malgorzata Nowicka Differential transcript usage and tuQTL analyses
with Dirichlet-multinomial model in RNA-seq Supplementary Page
edgeR Yunshun Chen
Aaron Lun
Davis McCarthy
Xiaobei Zhou
Mark D Robinson
Gordon Smyth
Empirical Analysis of Digital Gene Expression Data in R
FIRMAGene Mark D Robinson Analysis of differential splicing with Affymetrix Gene ST array data
flagme Mark D Robinson
Riccardo Romoli
Analysis of Metabolomics GC/MS Data
iCOBRA Charlotte Soneson Comparison and Visualization of Ranking and Assignment Methods
iSEE Charlotte Soneson
Aaron Lun
Federico Marini
Kevin Rue-Albrecht
Interactive SummarizedExperiment Explorer
muscat Helena L Crowell
Charlotte Soneson
Pierre-Luc Germain
Mark D Robinson
Multi-sample multi-group scRNA-seq data analysis tools
pipeComp Pierre-Luc Germain
Anthony Sonrel
Mark D Robinson
Pipeline benchmarking framework
regsplice Lukas M Weber L1-regularization based methods for detection of differential splicing
Repitools Mark D Robinson
Dario Strbenac
Aaron Statham
Andrea Riebler
Epigenomic tools (BayMeth)
scDblFinder Pierre-Luc Germain Identifies doublets in single-cell sequencing data
SpatialExperiment Helena L Crowell SpatialExperiment package provides an S4 class for Spatial Omics data handling.
treeclimbR Ruizhu Huang Search for the optimal level of a tree to interpret signal by combining with edgeR or DESeq2
TreeHeatmap Ruizhu Huang Visualize heatmaps at arbitrary levels of a tree.
TreeSummarizedExperiment Ruizhu Huang SummarizedExperiment-based object to store data with hierarchical structure

Data resources

Name Author(s) Description
Benchmark collection Robinson group Collection of high-throughput computational biology benchmarking data sets
conquer Charlotte Soneson Repository providing consistently processed
public single-cell RNA-seq data sets
DuoClustering2018 Angelo Duò
Charlotte Soneson
Data package with processed data and clustering results from Duò et al. (2018)
FlowRepository FR-FCM-ZZPH Lukas M Weber Data files for benchmark data sets used in “Comparison of clustering methods for high-dimensional single-cell flow and mass cytometry data” (Weber and Robinson, 2016)
FlowRepository FR-FCM-ZYL8 Lukas M Weber Data files for benchmark data sets used in our paper introducing the ‘diffcyt’ framework (Weber et al., 2018)
HDCytoData Lukas M Weber
Charlotte Soneson
Data package of high-dimensional cytometry data sets in
SummarizedExperiment and flowSet formats
TabulaMurisData Charlotte Soneson Bioconductor package providing access to scRNA-seq data from the Tabula Muris Consortium

Web applications

Name Author(s) Description
CATALYST Helena L Crowell Tools for preprocessing of cytometry data including
normalization, debarcoding, and compensation
CrispantCal Lukas M Weber R/Shiny web app to calculate injection mix volumes for
CRISPR-Cas9 experiments
CrispRVariantsLite Helen Lindsay Graphical user interface to the R/Bioconductor CrispRVariants package
iCOBRA Charlotte Soneson Graphical User interface to the R/Bioconductor iCOBRA package
pubassistant Reto Gerber
Mark D Robinson
Interactive explorer of publications and open access
scrnaseq_de_evaluation Charlotte Soneson Interactive browsing and exploration of the scRNA-seq differential expression results from Soneson and Robinson, 2018

Software & Workflows

Name Author(s) Description
ARMOR Stephany Orjuela
Ruizhu Huang
Katharina Hembach
Mark D Robinson
Charlotte Soneson
Snakemake workflow to perform an end-to-end RNA-seq analysis.
ARPEGGIO Stefan Milosavljevic
Tony Kuo
Samuele Decarli
Lucas Mohn
Jun Sese
Kentaro K. Shimizu
Rie Shimizu-Inatsugi
Mark D Robinson
SnakeMake workflow to analyse whole genome bisulfite sequencing data from allopolyploids.
gapless Stephan Schmeing Combined scaffolding, gap-closing and assembly correction with long reads.
ReSeq Stephan Schmeing More realistic simulator for genomic DNA sequences from Illumina machines that achieves a similar k-mer spectrum as the original sequences.

Other resources

Name Author(s) Description
ABCD-DNA Supplementary Page Mark D Robinson Supplementary Page with Supplementary Data (semi-processed), R Code for all Figures and analyses (Robinson et al., 2012).
conquer (build scripts) Charlotte Soneson
Mark D Robinson
Repository containing the code used to prepare the conquer (consistent quantification of external RNA-seq data sets) repository (Soneson and Robinson, 2018).
conquer (differential expression evaluation) Charlotte Soneson Repository containing the code used to perform the evalutaion of differential expression analysis methods in single-cell RNA-seq data (Soneson and Robinson, 2018) Supplementary Page
CrispRVariants (shiny app code) Helen Lindsay Repository containing the code underlying the CrispRVariantsLite Shiny-based web app (Lindsay et al, 2016).
cyTOF compensation Vito RT Zanotelli
Helena L Crowell
Mark D Robinson
Repository containing scripts to reproduce a majority of the figures from “Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry” (Chevrier et al., 2018).
cytometry-clustering-comparison Lukas M Weber Repository of scripts to reproduce and extend analyses and figures in “Comparison of clustering methods for high-dimensional single-cell flow and mass cytometry data” (Weber and Robinson, 2016)
diffcyt-evaluations Lukas M Weber Repository of scripts to reproduce evaluations and figures in our paper introducing the ‘diffcyt’ framework (Weber et al., 2018)
muscat-comparison Helena L Crowell Repository of scripts to reproduce comparisons and figures for ‘muscat’ framework (Crowell et al., 2019)
Differential splicing comparison Charlotte Soneson
Katharina Matthes
Repository containing the code for the comparison of various methods for differential isoform usage (differential splicing) detection (Soneson, Matthes et al., 2016) Supplementary Page.
edgeR robust Xiaobei Zhou Supplementary Page with Supplementary Data, R Code for simulations and analyses (Zhou et al., 2014).