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Shiny app for visualizing expresso results from v3, v4, and nf version of coffee+eXpresso pipelines

R environment for eXpresso RNA-seq differential expression analysis pipeline.

A R Shiny app for RNA-seq differential expression and gene set analysis across multiple contrasts.

Docker for Seurat5 and related scRNA-seq packages as well as ScanPy, SquidPy, and scvi-tools.

Docker for Oxford Nanopore Dorado

Environment and tools for Coffee RNA-seq alignment and quantitation pipeline

Docker for running 10x SpaceRanger. spaceranger --help

10x CellRanger docker. cellranger -h

Docker for NextFlow v23.10.1 for running nf-core and epi2me workflows.

Docker for running Oxford Nanopore's modkit software to create bedMethyl files

Docker for running IsoQuant on long read sequencing data.

Docker for Illumina DRAGEN Bio-IT platform version 3.9.3-8