Pinned Repositories
alevinQC
Create QC and summary reports for Alevin output
ARMOR
Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data
conquer_comparison
Code for evaluation of differential expression methods in single-cell RNA-seq data
countsimQC
countsimQC - Compare characteristic features of count data sets
ExploreModelMatrix
Explore design matrices interactively with R/Shiny
rna_velocity_quant
Evaluation of the effect of quantification choices on RNA velocity estimates
treeclimbR
einprot
Proteomics analysis workflows
mutscan
Software to process, statistically analyse and visualise deep mutational scanning data
iSEE
R/shiny interface for interactive visualization of data in SummarizedExperiment objects
csoneson's Repositories
csoneson/ARMOR
Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data
csoneson/ExploreModelMatrix
Explore design matrices interactively with R/Shiny
csoneson/alevinQC
Create QC and summary reports for Alevin output
csoneson/countsimQC
countsimQC - Compare characteristic features of count data sets
csoneson/treeclimbR
csoneson/iCOBRA
Interactive benchmarking of ranking and assignment methods
csoneson/compcodeR
csoneson/dreval
Convenience functions to evaluate reduced dimension representations in SingleCellExperiment objects
csoneson/TabulaMurisData
Access data from Tabula Muris Consortium via R/Bioconductor
csoneson/BiocStickers
Stickers for some Bioconductor packages - feel free to contribute and/or modify.
csoneson/galaxy-hub
Galaxy Community Hub
csoneson/bioc-actions
GitHub Actions for developing and maintaining Bioconductor packages
csoneson/bioc_pkg_licenses
csoneson/BiocPkgList
csoneson/csoneson.github.io
csoneson/exampleRPackage
csoneson/iSEE-example-data
csoneson/isee-lab-csama2025
csoneson/isee.bioconductor.org
Source control for configuration specific to isee.bioconductor.org
csoneson/iSEEindex
iSEE extension for a landing page to a custom collection of data sets
csoneson/mywebsite
csoneson/ngio
NGIO is a Python library to streamline OME-Zarr image analysis workflows.
csoneson/orthos_package_list
csoneson/peakCombiner
The fully R based tool peakCombiner is a user-friendly, transparent, modular and customizable package with the purpose to create a consensus peak file from genomic input regions. The aim is to allow even novice R users to create good quality combined peak sets to be used as the starting point for most downstream differential analyses.
csoneson/pyrasa
a package for spectral parametrization in python based on the IRASA algorithm
csoneson/S4Arrays
Foundation of array-like containers in Bioconductor
csoneson/sketchR_package_list
csoneson/substrateminer
A python package to discover enzyme substrates based on sequence consensus
csoneson/target-methylseq-qc
A lightweight pipeline for collecting Picard metrics from targeted sequence mapping files.
csoneson/test_biocmanager