nf-core

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146 repositories

marsseq
Public
MARS-seq v2 pre-processing pipeline with velocity
workflow pipeline nextflow single-cell single-cell-rna-seq nf-core star-solo mars-seq transcriptional-dynamics facs-sorting
Nextflow
•
MIT License
•3•6•3•1•Updated Nov 28, 2024Nov 28, 2024
spatialxe
Public
Nextflow
•
MIT License
•2•5•30•1•Updated Nov 28, 2024Nov 28, 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
•96•144•44•7•Updated Nov 28, 2024Nov 28, 2024
nanostring
Public
An analysis pipeline for Nanostring nCounter expression data.
workflow pipeline nextflow nanostring nanostringnorm nf-core
Nextflow
•
MIT License
•8•13•11•2•Updated Nov 28, 2024Nov 28, 2024
pacvar
Public
Longread PacBio sequencing processing for WGS and PureTarget
alignment long-read pacbio variant-calling wgs puretarget
Nextflow
•
MIT License
•1•1•0•2•Updated Nov 28, 2024Nov 28, 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
•723•284•451•184•Updated Nov 28, 2024Nov 28, 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
•191•242•258•36•Updated Nov 28, 2024Nov 28, 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
•36•128•41•4•Updated Nov 28, 2024Nov 28, 2024
references
Public
Nextflow
•
MIT License
•4•5•11•1•Updated Nov 28, 2024Nov 28, 2024
variantbenchmarking
Public
A nextflow variant benchmarking pipeline - premature
workflow benchmark pipeline nextflow draft variant-calling structural-variants nf-core
Nextflow
•
MIT License
•7•12•16•1•Updated Nov 28, 2024Nov 28, 2024
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
•37•64•58•4•Updated Nov 28, 2024Nov 28, 2024
website
Public
Code and files for the main nf-core website.
website nextflow nf-core
MDX
•
MIT License
•195•69•90•36•Updated Nov 28, 2024Nov 28, 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
•146•142•30•3•Updated Nov 28, 2024Nov 28, 2024
demultiplex
Public
Demultiplexing pipeline for sequencing data
nextflow illumina demultiplexing bcl2fastq nf-core bases2fastq elementbiosciences workflow pipeline
Nextflow
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MIT License
•38•44•17•1•Updated Nov 28, 2024Nov 28, 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•218•59•8•Updated Nov 28, 2024Nov 28, 2024
createtaxdb
Public
Parallelised and automated construction of metagenomic classifier databases of different tools
workflow database pipeline nextflow metagenomics profiling nf-core database-builder taxonomic-profiling metagenomic-profiling
Nextflow
•
MIT License
•5•7•16•2•Updated Nov 28, 2024Nov 28, 2024
scrnaseq
Public
A single-cell RNAseq pipeline for 10X genomics data
workflow rna-seq pipeline nextflow single-cell kallisto 10x-genomics 10xgenomics nf-core bustools
Nextflow
•
MIT License
•172•216•53•4•Updated Nov 28, 2024Nov 28, 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
•354•106•31•13•Updated Nov 28, 2024Nov 28, 2024
airrflow
Public
B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
nextflow nf-core b-cell repseq immcantation immunorepertoire airr workflow pipeline
Nextflow
•
MIT License
•35•54•20•4•Updated Nov 28, 2024Nov 28, 2024
setup-nextflow
Public
A GitHub action to install Nextflow
nextflow actions
TypeScript
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MIT License
•5•12•9•4•Updated Nov 28, 2024Nov 28, 2024
oncoanalyser
Public
A comprehensive cancer DNA/RNA analysis and reporting pipeline
workflow pipeline nextflow nf-core
Nextflow
•
MIT License
•8•50•14•3•Updated Nov 28, 2024Nov 28, 2024
configs
Public
Config files used to define parameters specific to compute environments at different Institutions
bioinformatics nextflow configuration pipelines workflows nf-core
Nextflow
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MIT License
•276•88•12•16•Updated Nov 28, 2024Nov 28, 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•46•9•5•Updated Nov 27, 2024Nov 27, 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•196•13•4•Updated Nov 27, 2024Nov 27, 2024
proteinfold
Public
Protein 3D structure prediction pipeline
nextflow protein-structure protein-sequences protein-folding protein-fold-prediction nf-core alphafold2 workflow pipeline
Nextflow
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MIT License
•39•60•25•3•Updated Nov 27, 2024Nov 27, 2024
multiplesequencealign
Public
A pipeline to run and systematically evaluate Multiple Sequence Alignment (MSA) methods.
workflow pipeline nextflow nf-core
Nextflow
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MIT License
•11•22•5•1•Updated Nov 27, 2024Nov 27, 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 Nov 26, 2024Nov 26, 2024
rangeland
Public
Pipeline for remotely sensed imagery. The pipeline processes satellite imagery alongside auxiliary data in multiple steps to arrive at a set of trend files related to land-cover changes.
workflow pipeline nextflow landsat trends satellite-imagery earth-observation trend-analysis spectral-unmixing nf-core
Nextflow
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MIT License
•3•5•0•2•Updated Nov 26, 2024Nov 26, 2024
tumourevo
Public
Analysis pipleine to model tumour clonal evolution from WGS data (driver annotation, quality control of copy number calls, subclonal and mutational signature deconvolution)
quality-control cancer-genomics population-genetics copy-number-variation variant-annotation mutational-signatures cancer-evolution subclonal-deconvolution
GNU General Public License v3.0
•2•2•9•0•Updated Nov 26, 2024Nov 26, 2024
dualrnaseq
Public
Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.
workflow rna-seq pipeline nextflow quantification nf-core host-pathogen dualrna-seq readmapping
Nextflow
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MIT License
•30•18•15•8•Updated Nov 26, 2024Nov 26, 2024