nf-core

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148 repositories

differentialabundance
Public
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
workflow rna-seq pipeline nextflow shiny deseq2 microarray chip-seq atac-seq differential-expression
Nextflow
•
MIT License
•40•66•75•7•Updated Dec 26, 2024Dec 26, 2024
modules
Public
Repository to host tool-specific module files for the Nextflow DSL2 community!
modules nextflow pipelines workflows nf-core dsl2 nf-test
Nextflow
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MIT License
•735•287•464•191•Updated Dec 26, 2024Dec 26, 2024
ops
Public
Python
•2•1•48•9•Updated Dec 26, 2024Dec 26, 2024
smrnaseq
Public
A small-RNA sequencing analysis pipeline
workflow pipeline nextflow small-rna nf-core smrna-seq
Nextflow
•
MIT License
•127•76•10•1•Updated Dec 26, 2024Dec 26, 2024
test-datasets
Public
Test data to be used for automated testing with the nf-core pipelines
testing workflow nextflow test-data nf-core pipelines test-datasets
MIT License
•361•109•31•14•Updated Dec 26, 2024Dec 26, 2024
chipseq
Public
ChIP-seq peak-calling, QC and differential analysis pipeline.
workflow chip nf-core peak-calling pipeline nextflow chip-seq macs2 chromatin-immunoprecipitation
Nextflow
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MIT License
•150•200•16•5•Updated Dec 26, 2024Dec 26, 2024
rnafusion
Public
RNA-seq analysis pipeline for detection of gene-fusions
workflow rna-seq pipeline nextflow gene-fusion fusion rna fusion-genes nf-core
Nextflow
•
MIT License
•98•148•41•4•Updated Dec 26, 2024Dec 26, 2024
website
Public
Code and files for the main nf-core website.
website nextflow nf-core
MDX
•
MIT License
•194•70•93•40•Updated Dec 26, 2024Dec 26, 2024
configs
Public
Config files used to define parameters specific to compute environments at different Institutions
bioinformatics nextflow configuration pipelines workflows nf-core
Nextflow
•
MIT License
•277•90•12•15•Updated Dec 24, 2024Dec 24, 2024
pacvar
Public
Longread PacBio sequencing processing for WGS and PureTarget
alignment long-read pacbio variant-calling wgs puretarget
Nextflow
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MIT License
•1•1•1•4•Updated Dec 24, 2024Dec 24, 2024
scnanoseq
Public
Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics
nanopore nextflow scrna-seq single-cell 10xgenomics nf-core long-read-sequencing
Nextflow
•
MIT License
•6•21•1•1•Updated Dec 24, 2024Dec 24, 2024
setup-nextflow
Public
A GitHub action to install Nextflow
nextflow actions
TypeScript
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MIT License
•5•12•8•6•Updated Dec 24, 2024Dec 24, 2024
nascent
Public
Nascent Transcription Processing Pipeline
nextflow rna transcription tss gro-seq nf-core pro-seq nascent workflow pipeline
Nextflow
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MIT License
•10•18•37•4•Updated Dec 23, 2024Dec 23, 2024
methylseq
Public
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
workflow pipeline nextflow dna-methylation rrbs methyl-seq epigenomics bisulfite-sequencing nf-core epigenome
Nextflow
•
MIT License
•145•150•22•4•Updated Dec 23, 2024Dec 23, 2024
scdownstream
Public
A single cell transcriptomics pipeline for QC, integration and making the data presentable
quality-control integration clustering dimensionality-reduction single-cell scverse
Nextflow
•
MIT License
•13•44•25•3•Updated Dec 23, 2024Dec 23, 2024
funcscan
Public
(Meta-)genome screening for functional and natural product gene sequences
workflow bioinformatics pipeline nextflow amp assembly function metagenomics amr screening
Nextflow
•
MIT License
•21•75•16•3•Updated Dec 23, 2024Dec 23, 2024
oncoanalyser
Public
A comprehensive cancer DNA/RNA analysis and reporting pipeline
workflow pipeline nextflow nf-core
Nextflow
•
MIT License
•9•54•14•3•Updated Dec 23, 2024Dec 23, 2024
fastqrepair
Public
A 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
corruption fastq-format fastq data-cleaning data-recovery well-formed recovery-tool fastq-corrupted unpaired-reads reads-interleaving
Nextflow
•
MIT License
•1•1•5•1•Updated Dec 22, 2024Dec 22, 2024
references
Public
Nextflow
•
MIT License
•4•7•13•0•Updated Dec 22, 2024Dec 22, 2024
stats
Public
evidence
HTML
•0•0•9•10•Updated Dec 21, 2024Dec 21, 2024
rnaseq
Public
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
workflow rna-seq pipeline nextflow rna nf-core
Nextflow
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MIT License
•713•944•63•12•Updated Dec 21, 2024Dec 21, 2024
tools
Public
Python package with helper tools for the nf-core community.
bioinformatics linting linter nf-core python workflow pipeline nextflow
Python
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MIT License
•192•245•271•33•Updated Dec 20, 2024Dec 20, 2024
riboseq
Public
Pipeline for the analysis of ribosome profiling, or Ribo-seq (also named ribosome footprinting) data.
workflow pipeline nextflow nf-core
Nextflow
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MIT License
•7•11•13•1•Updated Dec 20, 2024Dec 20, 2024
denovotranscript
Public
A pipeline for de novo transcriptome assembly of paired-end short reads from bulk RNA-seq
rna-seq transcriptome denovo-assembly
Nextflow
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MIT License
•3•9•3•1•Updated Dec 20, 2024Dec 20, 2024
troughgraph
Public
A quantitative assessment of the underlying permafrost landscapes and, per extension, of the level of permafrost thaw in the region
Nextflow
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MIT License
•0•2•0•1•Updated Dec 20, 2024Dec 20, 2024
taxprofiler
Public
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
workflow bioinformatics nanopore pipeline nextflow shotgun pathogen metagenomics classification profiling
Nextflow
•
MIT License
•37•132•39•8•Updated Dec 20, 2024Dec 20, 2024
pixelator
Public
Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)
nextflow proteins pixelator single-cell nf-core single-cell-omics molecular-pixelation pixelgen-technologies workflow pipeline
Nextflow
•
MIT License
•3•8•0•2•Updated Dec 20, 2024Dec 20, 2024
pathogensurveillance
Public
Surveillance of pathogens using population genomics and sequencing
workflow pipeline nextflow nf-core
HTML
•
MIT License
•5•14•41•1•Updated Dec 20, 2024Dec 20, 2024
mag
Public
Assembly and binning of metagenomes
workflow nanopore annotation nextflow metagenomics binning nanopore-sequencing nf-core long-read-sequencing bioinformatics
Nextflow
•
MIT License
•111•219•63•9•Updated Dec 20, 2024Dec 20, 2024
rnasplice
Public
rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis
workflow rna-seq pipeline nextflow alternative-splicing rna nf-core splicing
Nextflow
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MIT License
•28•48•9•3•Updated Dec 20, 2024Dec 20, 2024