About us:

• Our homepage at FMI    

• Our group page at SIB    

Teaching material

• SIB Advanced topics in single-cell analysis - 2022
  Course homepage | Course repository

• Joint SIB / SciLifeLab Advanced topics in single-cell omics - 2021
  Course homepage | Course repository

• SIB Advanced topics in single-cell transcriptomics - 2020
  Course homepage | Course repository

• Joint SIB / SciLifeLab Autumn School Single Cell Analysis - 2019
  Course homepage | Course repository

• SIB Single-cell RNA-Seq Analysis - 2018
  Course homepage | Course handout

Public software and data

• QuasR: Quantification and Annotation of Short reads in R
  Bioconductor landing page | PubMed | free HTML | free PDF
  GitHub repo

• Rbowtie: R wrapper around the popular bowtie short read aligner
  Bioconductor landing page | PubMed | free HTML | free PDF
  GitHub repo

• Rhisat2: R wrapper around the hisat2 aligner
  Bioconductor landing page | GitHub repo

• MethylSeekR: Identification of active regulatory regions from DNA methylation data
  Bioconductor landing page | PubMed | free HTML | free PDF
  GitHub repo

• monaLisa: Motif Enrichment Analysis and Visualization
  Bioconductor landing page | PubMed | GitHub repo

• griph: Graph Inference of Population Heterogeneity
  GitHub repo

• swissknife: Handy code shared in the FMI CompBio group
  GitHub repo

• alevinQC: Generation of QC and summary reports for alevin and alevin-fry output Bioconductor landing page | GitHub repo

• galaxy2shiny2galaxy: Combining Galaxy with an external Shiny server GitHub page

• ExploreModelMatrix: Interactive exploration of design matrices in R.
  Bioconductor landing page | PubMed | free full-text | GitHub repo

• eisaR: Exon-Intron Split Analysis and methods for extracting transcript coordinates and sequences
  Bioconductor landing page | GitHub repo

• TabulaMurisSenisData: Access to bulk and single-cell RNA-seq data from the Tabula Muris Senis project in SingleCellExperiment format
  Bioconductor landing page | GitHub repo

• sketchR: An R interface for python subsampling/sketching algorithms
  Bioconductor landing page | GitHub repo

• mutscan: An R package for processing, statistical analysis and visualization of Multiplexed Assays of Variant Effect data
  PubMed | free full-text | GitHub repo

• einprot: A collection of workflows for statistical analysis of quantitative proteomics data
  free full-text | GitHub repo

• orthos: Mechanistic insights from differential gene expression experiments with Deep Generative Networks
  Bioconductor landing page | GitHub repo

• orthosData: Companion package to orthos, providing access to data objects required for the methods therein
  Bioconductor landing page | GitHub repo

Supplementary information

• COSIE: COrrected Splicing Indices for Exon arrays
  supplementary data and R code | PubMed | free HTML | free PDF

• GLD-1 Binding Motif (GBM) finder
  supplementary R code

• MethylSeekR
  supplementary data

• EISA: Exon-Intron Split Analysis (see also eisaR package above)
  supplementary data and R code | PubMed | HTML | PDF

Software build status

… is available here.