U-BDS/scnanoseq Fork of nf-core/scnanoseq

Single-cell/nuclei pipeline for data derived from Oxford Nanopore

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mahesh-panchal/nf-metaomics-daisychain

A meta-pipeline of nf-core pipelines for meta-omic analysis.

Language: Nextflow - Size: 624 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 3 - Forks: 2

nf-core/fastquorum

Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)

Language: Nextflow - Size: 5.13 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 23 - Forks: 16

Multiomics-Analytics-Group/nf-vuegen

nf-core module designed to automate report generation from outputs produced by other modules, subworkflows, or pipelines. VueGen creates reports from bioinformatics outputs, supporting formats like PDF, HTML, DOCX, ODT, PPTX, Reveal.js, Jupyter notebooks, and Streamlit web applications.

Language: Nextflow - Size: 3.16 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 2 - Forks: 0

Midnighter/nf-core-adr

Structurizr documentation of nf-core

Language: ASL - Size: 22.5 KB - Last synced at: about 2 months ago - Pushed at: about 3 years ago - Stars: 4 - Forks: 1

nf-core/hicar

Pipeline for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.

Language: Nextflow - Size: 34.7 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 10 - Forks: 8

nf-core/lncpipe Fork of likelet/LncPipe

UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets

Language: Nextflow - Size: 29.6 MB - Last synced at: about 2 months ago - Pushed at: 4 months ago - Stars: 34 - Forks: 25

nf-core/hgtseq

A pipeline to investigate horizontal gene transfer from NGS data

Language: Nextflow - Size: 5.11 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 25 - Forks: 7

nf-core/spinningjenny

Pipeline for simulating the first industrial revolution using Agent Based Models.

Language: Nextflow - Size: 2.55 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 4 - Forks: 4

nf-core/rnasplice

rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis

Language: Nextflow - Size: 160 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 54 - Forks: 32

nf-core/riboseq

Pipeline for the analysis of ribosome profiling, or Ribo-seq (also named ribosome footprinting) data.

Language: Nextflow - Size: 19.8 MB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 13 - Forks: 11

nf-core/rangeland

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.

Language: Nextflow - Size: 4.72 MB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 7 - Forks: 6

nf-core/rnadnavar

Pipeline for RNA and DNA integrated analysis for somatic mutation detection

Language: Nextflow - Size: 4.18 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 8 - Forks: 9

nf-core/phyloplace

nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.

Language: Nextflow - Size: 3.43 MB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 10 - Forks: 5

nf-core/radseq

Variant-calling pipeline for Restriction site-associated DNA sequencing (RADseq).

Language: Nextflow - Size: 2.66 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 7 - Forks: 6

nf-core/phageannotator

Pipeline for identifying, annotation, and quantifying phage sequences in (meta)-genomic sequences.

Language: Nextflow - Size: 5.18 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 13 - Forks: 9

nf-core/molkart

A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)

Language: Nextflow - Size: 6.57 MB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 12 - Forks: 12

nf-core/nanostring

An analysis pipeline for Nanostring nCounter expression data.

Language: Nextflow - Size: 4.53 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 14 - Forks: 12

nf-core/metapep

From metagenomes to epitopes and beyond

Language: Nextflow - Size: 8.4 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 12 - Forks: 7

nf-core/hic

Analysis of Chromosome Conformation Capture data (Hi-C)

Language: Nextflow - Size: 3.74 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 99 - Forks: 60

nf-core/kmermaid

k-mer similarity analysis pipeline

Language: Nextflow - Size: 12.8 MB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 21 - Forks: 13

nf-core/dualrnaseq

Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.

Language: Nextflow - Size: 45 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 22 - Forks: 36

nf-core/datasync

nf-core/datasync is a system operation pipeline that provides several workflows for handling system operation / automation tasks

Language: Nextflow - Size: 613 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 9 - Forks: 3

nf-core/cutandrun

Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.

Language: Nextflow - Size: 8.66 MB - Last synced at: 2 months ago - Pushed at: 3 months ago - Stars: 91 - Forks: 52

nf-core/atacseq

ATAC-seq peak-calling and QC analysis pipeline

Language: Nextflow - Size: 9.72 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 200 - Forks: 125

borgessbarbara/TranscriptClean-NF

An implementation of TranscriptClean tool into a Nextflow module

Size: 0 Bytes - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

nf-core/gh-actions-lint 📦

GitHub Action to run nf-core code linting on a Nextflow pipeline

Language: Shell - Size: 9.77 KB - Last synced at: 20 days ago - Pushed at: over 2 years ago - Stars: 5 - Forks: 4

davetang/rnaseq

RNA-seq analyses.

Language: Shell - Size: 5.52 MB - Last synced at: 14 days ago - Pushed at: 9 months ago - Stars: 9 - Forks: 5

nf-core/vscode-extensionpack

A VSCode extension pack for nf-core developers.

Size: 240 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 14 - Forks: 7

natanast/nextflow_scripts

This repository includes some simple workflows written in Nextflow.

Language: Nextflow - Size: 5.86 KB - Last synced at: 5 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

georgiesamaha/configBuilder-nf

Nextflow config builder scripts for supported HPC infrastructures.

Language: Python - Size: 82 KB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 8 - Forks: 1

bigbio/pgdb

ProteomeGenomics Database Creation - Nextflow Pipeline

Language: Nextflow - Size: 2.9 MB - Last synced at: 2 months ago - Pushed at: about 3 years ago - Stars: 2 - Forks: 11

nf-core/pgdb Fork of bigbio/pgdb

The ProteoGenomics database generation workflow creates different protein databases for ProteoGenomics data analysis.

Language: Nextflow - Size: 3.07 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 5 - Forks: 8

nf-core/sublime Fork of peterk87/sublime-nextflow

Nextflow workflow syntax highlighting and snippets for Sublime Text 4

Language: Python - Size: 654 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 6 - Forks: 4

nf-core/variantcatalogue

Pipeline to generate variant catalogues, a list of variants and their frequencies in a population, from whole genome sequences.

Language: Nextflow - Size: 184 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 9 - Forks: 4

U-BDS/training_guides

Compilation of training guides

Language: Shell - Size: 7.1 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 4 - Forks: 0

nf-core/viralintegration

Analysis pipeline for the identification of viral integration events in genomes using a chimeric read approach.

Language: Python - Size: 3.37 MB - Last synced at: 2 months ago - Pushed at: about 1 year ago - Stars: 17 - Forks: 9

santorsola-teaching/class-lab-adv-omics

Repository for the Course "Laboratory of Advanced Bioinformatics for Omics Sciences", in the Curriculum "Molecular and Digital Biology" of the M.Sc. Molecular Biology and Genetics, University of Pavia

Language: HTML - Size: 299 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 3 - Forks: 1

nf-core/clipseq

CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.

Language: Nextflow - Size: 64.8 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 21 - Forks: 40

carpentries-incubator/workflows-nextflow

Workflow management with Nextflow and nf-core

Language: Nextflow - Size: 20.9 MB - Last synced at: 2 months ago - Pushed at: 6 months ago - Stars: 25 - Forks: 38

srikanth-srinvas/dragonflye-hybrid-genome-assembly

Nextflow-powered Dragonflye Pipeline for Assembling Genomes from Nanopore and Illumina Reads

Language: Nextflow - Size: 224 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

nf-core/imcyto

Image Mass Cytometry analysis pipeline

Language: Python - Size: 8.85 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 25 - Forks: 18

nf-core/circdna

Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.

Language: Python - Size: 184 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 28 - Forks: 14

phac-nml/iridanextexample

An example pipeline for running on IRIDA Next

Language: Nextflow - Size: 2.49 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 3

sateeshperi/nextflow_varcal

Nextflow Tutorial - Variant Calling Edition

Language: HTML - Size: 70 MB - Last synced at: 24 days ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 3

dgrfs/NFCore_RNASeq_Cardiff_University_Hawk

RNA Sequencing pipeline on Cardiff University Hawk using NF-Core with example data.

Language: Shell - Size: 22.1 MB - Last synced at: 23 days ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

seqeralabs/conda-recipes 📦

Conda recipes for the Eel project

Language: Shell - Size: 215 KB - Last synced at: 10 days ago - Pushed at: about 1 year ago - Stars: 3 - Forks: 1

nf-core/scflow Fork of combiz/nf-core-scflow 📦

Please consider using/contributing to https://github.com/nf-core/scdownstream

Language: Nextflow - Size: 3.14 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 24 - Forks: 9

wassimsalam01/thesis

nf-core/methylseq methylation (Bisulfite-Sequencing) analysis pipeline using custom Bismark settings + Bismark cytosine reports analysis using Daphnia-adapted DMRichR pipeline

Language: Shell - Size: 2.06 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

nf-core/omicsgenetraitassociation

A nextflow pipeline which integrates multiple omic data streams and performs coordinated analysis

Language: Nextflow - Size: 2.9 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 2

nf-core/diaproteomics

Automated quantitative analysis of DIA proteomics mass spectrometry measurements.

Language: Nextflow - Size: 4.06 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 12 - Forks: 11

nf-core/genomeannotator

Pipeline for the identification of (coding) gene structures in draft genomes.

Language: Nextflow - Size: 97 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 15 - Forks: 11

nf-core/slamseq Fork of t-neumann/slamseq

SLAMSeq processing and analysis pipeline

Language: Nextflow - Size: 4.46 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 5 - Forks: 7

nf-core/quantms 📦

Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.

Language: Nextflow - Size: 21.5 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 26 - Forks: 28

Midnighter/nf-file-utils 📦

Query files for their type and compression state.

Language: Groovy - Size: 2.93 KB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 1

nf-core/metaboigniter

Pre-processing of mass spectrometry-based metabolomics data with quantification and identification based on MS1 and MS2 data.

Language: Nextflow - Size: 46.1 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 15 - Forks: 14

PRIDE-Archive/pride-molecule-indexer

NextFlow and NF-Core workflow that convert PRIDE Complete submissions to json files including PSMs, Peptides and Proteins.

Language: Java - Size: 303 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 1

opencobra/jeweler

Test and grade genome-scale metabolic models (GEMs).

Language: Nextflow - Size: 2.16 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

nf-wrap/main

Nextflow wrapper built around nf-core/modules

Language: Nextflow - Size: 2.22 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 11 - Forks: 5

littleblackfish/apis-methylation

DNA methylation in the honey bee and some other Hymenopterans

Language: Jupyter Notebook - Size: 1.79 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 1 - Forks: 0

nf-core/vale

Spelling and grammar linting for nf-core documentation

Size: 16.6 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

nf-core/denovohybrid Fork of caspargross/nf-core-denovohybrid 📦

UNDER CONSTRUCTION: Hybrid genome assembly pipeline using a combination of long and short sequencing reads

Language: Nextflow - Size: 2.55 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 8 - Forks: 3

nf-core/cageseq

CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.

Language: Nextflow - Size: 4.02 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 10 - Forks: 11

nf-core/exoseq 📦

Please consider using/contributing to https://github.com/nf-core/sarek

Language: Nextflow - Size: 2.77 MB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 14 - Forks: 25

nf-core/neutronstar 📦

De novo assembly pipeline for 10X linked-reads using Supernova

Language: Nextflow - Size: 71.3 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 4 - Forks: 5

nf-core/deepvariant Fork of lifebit-ai/DeepVariant 📦

Please consider using/contributing to https://github.com/nf-core/sarek

Language: Nextflow - Size: 7.18 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 40 - Forks: 18

rhinosys/ampliseq Fork of nf-core/ampliseq

Amplicon sequencing analysis workflow using DADA2 and QIIME2

Size: 10.4 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

nf-core/mnaseseq

MNase-seq analysis pipeline using BWA and DANPOS2.

Language: Nextflow - Size: 4.53 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 10 - Forks: 8

nf-core/smartseq2 Fork of icbi-lab/smartseq2_pipeline 📦

A pipeline for processing single cell RNA-seq data generated with the SmartSeq2 protocol.

Language: Nextflow - Size: 2.45 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 15 - Forks: 10

nf-core/prettier-plugin-nextflow

Language: JavaScript - Size: 318 KB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 4 - Forks: 0

nf-core/tower-action Fork of ewels/tower-action 📦

GitHub Action to launch a workflow using Nextflow Tower.

Language: Shell - Size: 833 KB - Last synced at: 15 days ago - Pushed at: over 2 years ago - Stars: 12 - Forks: 6

nf-core/ssds 📦

Single-stranded DNA Sequencing (SSDS) nf-core pipeline

Language: Nextflow - Size: 2.28 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 2

nf-core/crisprvar 📦

[WIP] Evaluate outcomes from genome editing experiments

Language: Nextflow - Size: 84.3 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 5 - Forks: 3

nf-core/liverctanalysis Fork of luiskuhn/liverctanalysis 📦

UNDER CONSTRUCTION: pipeline for liver CT analysis

Size: 2.35 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

Midnighter/nf-join-map

Demonstrate problems with merging channels using a map as the key to merge by.

Language: Nextflow - Size: 16.6 KB - Last synced at: 3 days ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

nf-core/vipr 📦

Assembly and intrahost / low-frequency variant calling for viral samples

Language: Nextflow - Size: 217 KB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 14 - Forks: 10

Open-Science-Community-Saudi-Arabia/moleculardymics

This workflow for molecular dynamics simulation of proteins

Language: Groovy - Size: 2.16 MB - Last synced at: about 14 hours ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 2

nf-core/ddamsproteomics Fork of glormph/nf-core-dda-quant-proteomics 📦

Quantitative shotgun MS proteomics

Language: Nextflow - Size: 25.1 MB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 4 - Forks: 0

lgi-onehealth/ref-match-db

A nextflow workflow to build referenceseeker DBs on the fly

Language: Nextflow - Size: 26.4 KB - Last synced at: over 2 years ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0

ulelab/peka-eclip

Download and prepare ENCODE eCLIP raw fastq for processing with the nf-core/clipseq pipeline

Language: Nextflow - Size: 37.1 KB - Last synced at: 4 months ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 3

BarryDigby/circrna Fork of nf-core/circrna

nf-core/circrna dev

Language: Perl - Size: 53.7 MB - Last synced at: over 2 years ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 0

MatthiasZepper/nfcore_stats_backend

An application to gather statistics for the nf-core community, build with FastAPI, Pydantic, Celery and SQLAlchemy.

Language: Python - Size: 141 KB - Last synced at: 10 days ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

sguizard/nf-core-isoseq Fork of nf-core/isoseq

Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed annotation.

Language: Nextflow - Size: 3.61 MB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

Midnighter/sratools-settings-poc

Proof of concept showing a different way to handle the NCBI settings.

Language: Nextflow - Size: 2.93 KB - Last synced at: 5 months ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

erikrikarddaniel/magmap

Nextflow (nf-core) workflow for mapping reads to large collections of genomes.

Language: Nextflow - Size: 2.26 MB - Last synced at: 2 months ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 1

ajodeh-juma/ngs-academy-africa-nfcore

Advanced Training in Bioinformatics Workflows: Beginner - Intermediate level Bioinformaticians working with next-generation sequencing data in East-Africa.

Language: Nextflow - Size: 2.83 MB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

SusiJo/master_project

Processing of RNA-Seq data with nf-core pipelines and machine learning

Language: Python - Size: 3.99 MB - Last synced at: over 2 years ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 0

drpatelh/nf-core-atacseq Fork of nf-core/atacseq

See the main fork of this repository here >>>

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drpatelh/nf-core-mnaseseq Fork of nf-core/mnaseseq

See the main fork of this repository here >>>

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csawye01/nf-core-demultiplex

Demultiplexing pipeline for sequencing data

Language: Nextflow - Size: 367 KB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 1

csawye01/nanoseq Fork of nf-core/nanoseq

See the main fork of this repository here >>> https://github.com/nf-core/nanoseq

Language: Nextflow - Size: 1.79 MB - Last synced at: over 2 years ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 0

andreas-wilm/nf-core-bacass Fork of nf-core/bacass

Simple bacterial assembly and annotation pipeline

Language: Nextflow - Size: 757 KB - Last synced at: over 2 years ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 0

drpatelh/nf-core-mrimorph

UNDER CONSTRUCTION: Mouse brain morphometry analysis pipeline for MRI imaging data

Language: Nextflow - Size: 127 KB - Last synced at: 5 months ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 1

abhi18av/cookiecutter-nextflow

Language: Nextflow - Size: 191 KB - Last synced at: 5 months ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

drpatelh/nf-core-sgrnaquant

UNDER CONSTRUCTION: CRISPR sgRNA quantification pipeline

Language: Nextflow - Size: 64.5 KB - Last synced at: 5 months ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0