Software & Resources
OMNIBENCHMARK FRAMEWORK: 
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). |