About us:
Teaching material
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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
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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
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galaxy2shiny2galaxy: Combining Galaxy with an external Shiny server GitHub page
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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 -
ez-zarr: Python package providing easy, high-level access to OME-Zarr filesets
PyPI landing page | GitHub repo
Supplementary information
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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.