nf-core
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Public- Config files used to define parameters specific to compute environments at different Institutions
- Generation and update of protein families
- A pipeline for de novo transcriptome assembly of paired-end short reads from bulk RNA-seq
scdownstream
PublicA single cell transcriptomics pipeline for QC, integration and making the data presentable- Pipeline for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, to analyze chromatin state.
- An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
stats
Publicreferences
Publicmag
PublicAssembly and binning of metagenomescreatetaxdb
PublicParallelised and automated construction of metagenomic classifier databases of different tools- Call and score variants from WGS/WES of rare disease patients.
rnafusion
Public- Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)
spatialvi
PublicPipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.logos
Publicsetup-nextflow
Publiconcoanalyser
Publicfastqrepair
PublicA pipeline that can be used to recover corrupted FASTQ.gz files, drop or fix uncompliant reads, remove unpaired reads, and settles reads that became disordered- Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics
kmermaid
Publicrnavar
Public