JaneliaSciComp/exllsm-circuit-reconstruction

Nextflow pipeline encapsulating workflows for analyzing expansion lattice light-sheet microscopy (ExLLSM) imagery

Language: Nextflow - Size: 1.24 MB - Last synced at: 13 days ago - Pushed at: 2 months ago - Stars: 13 - Forks: 1

CFSAN-Biostatistics/bettercallsal

Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.

Language: Nextflow - Size: 52.6 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 11 - Forks: 2

stracquadaniolab/apex-nf

APEX: Automated Protein EXpression in E. coli

Language: Python - Size: 39.8 MB - Last synced at: 2 months ago - Pushed at: 3 months ago - Stars: 2 - Forks: 0

nschan/nf-genomeassembly

Nextflow pipeline to assemble genomes from long reads.

Language: Nextflow - Size: 1000 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 3 - Forks: 0

replikation/What_the_Phage

WtP: Phage identification via nextflow and docker or singularity

Language: Nextflow - Size: 40.9 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 105 - Forks: 15

Sydney-Informatics-Hub/Bioinformatics

A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common methods.

Size: 173 KB - Last synced at: 4 days ago - Pushed at: 4 months ago - Stars: 17 - Forks: 1

CFSAN-Biostatistics/cronology

cronology is an automated workflow for Cronobacter whole genome sequence assembly, subtyping and isolate clustering based on NCBI Pathogen Detection Project for Cronobacter.

Language: Nextflow - Size: 16.2 MB - Last synced at: 2 months ago - Pushed at: 11 months ago - Stars: 3 - Forks: 2

adamd3/BactSeq

A nextflow pipeline for performing bacterial RNA-Seq data analysis.

Language: Nextflow - Size: 2.32 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 8 - Forks: 1

LieberInstitute/SPEAQeasyWorkshop2020

EuroBioc2020 SPEAQeasy workshop https://eurobioc2020.bioconductor.org by Nick Eagles and Josh Stolz. For more information about SPEAQeasy check http://research.libd.org/SPEAQeasy/. For an example on how to use this RNA-seq processing pipeline and analyze the output files check http://research.libd.org/SPEAQeasy-example/.

Language: R - Size: 13.9 MB - Last synced at: 2 months ago - Pushed at: 6 months ago - Stars: 3 - Forks: 0

utdal/Bulk-RNA-Seq-Nextflow-Pipeline

This is an automated workflow pipeline for analyzing and processing Bulk-RNA seq data, implemented primarily in bash, python and R, and wrapped in a NextFlow workflow to characterize the gene landscape in the samples.

Language: Nextflow - Size: 4.24 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

JBris/nextflow-graph-machine-learning

A Nextflow pipeline demonstrating how to train graph neural networks for gene regulatory network reconstruction using DREAM5 data.

Language: Python - Size: 5.69 MB - Last synced at: about 1 month ago - Pushed at: 7 months ago - Stars: 5 - Forks: 1

pritampanda15/NGS-Workflows

Next-generation Sequencing workflows

Language: Jupyter Notebook - Size: 275 MB - Last synced at: 5 days ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

adamd3/StrainQuant

A Nextflow pipeline for performing bacterial RNA-Seq analysis without a reference genome.

Language: Nextflow - Size: 30.7 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 1 - Forks: 0

Aveglia/vAMPirus

Automated virus amplicon sequencing analysis program integrated with Nextflow pipeline manager.

Language: Nextflow - Size: 28 MB - Last synced at: 3 months ago - Pushed at: about 1 year ago - Stars: 9 - Forks: 3

igsr/igsr_analysis

This repo contains code that is relevant for the analysis (Mapping, BAM qc, Variant Calling, Filtering etc...) of IGSR data

Language: Jupyter Notebook - Size: 15.6 MB - Last synced at: 23 days ago - Pushed at: over 2 years ago - Stars: 4 - Forks: 5

zqbake/hictools

Tools for processing HIC data.

Language: Python - Size: 16.5 MB - Last synced at: 16 days ago - Pushed at: about 4 years ago - Stars: 11 - Forks: 2

gavinf97/thesisreal

My final thesis project work from my Biomedical Genomics MSc undertaken at NUIG, 2021. Includes Nextflow, Snakemake, Bash, Python and R scripts.

Language: Jupyter Notebook - Size: 960 KB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0

manuelesimi/hello-nextflow

A simple pipeline to test some basic nextflow features.

Language: Nextflow - Size: 115 KB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

JBris/nextflow-tutorials

Working through NextFlow tutorials. See https://github.com/nextflow-io/training

Language: HTML - Size: 2.57 MB - Last synced at: 4 months ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

azavea/pipeline-playground

A repository with usage examples of various pipeline and workflow orchestration tools

Language: HCL - Size: 3.01 MB - Last synced at: 4 months ago - Pushed at: about 4 years ago - Stars: 2 - Forks: 1

vickylaram/NGSeq_Quality_Visualization

A nextflow pipeline for analysis and visualisation of NGS data using FastQC and Python Ploty Dash.

Language: Python - Size: 9.95 MB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

asadprodhan/phyloTree

Bayesian phylogenetic analysis

Language: Nextflow - Size: 34.2 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

czbiohub-sf/nf-kmer-similarity Fork of nf-core/kmermaid

Language: Nextflow - Size: 8.54 MB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0

cobinet/HLA_lli

HLA typing pipelines in nextflow

Language: Nextflow - Size: 36.1 KB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0

GaitiLab/nf-processes

modules for processing and analyzing single cell data using Nextflow

Language: Nextflow - Size: 106 KB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 1

rajanbit/Bioinfo_nf_Scripts

Nextflow Scripts/Workflows for Bioinformatics

Language: Nextflow - Size: 6.84 KB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

ifremer-bioinformatics/orson

Workflow for prOteome and tRanScriptome functiOnal aNnotation. CAUTION : project has moved to Gitlab.

Language: Nextflow - Size: 1.2 MB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 5 - Forks: 3

Open-Science-Community-Saudi-Arabia/moleculardymics

This workflow for molecular dynamics simulation of proteins

Language: Groovy - Size: 2.16 MB - Last synced at: 3 days ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 2

Jianhua-Wang/GWAS-pipeline

From QC to summary statistics

Language: HTML - Size: 26.4 MB - Last synced at: over 2 years ago - Pushed at: almost 5 years ago - Stars: 11 - Forks: 3

TheSergeyPixel/nf_target

Nextflow pipeline for targeted sequencing data.

Language: Nextflow - Size: 499 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

elowy01/vcf_filtering

Filter a VCF to discard false positive variants

Language: Python - Size: 72.3 KB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 6 - 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: over 2 years ago - Stars: 1 - Forks: 0

BU-ISCIII/nextflow-scif

This is a demo about how to develop and deploy a pipeline using nextflow, scif, a container (Singularity and Docker) and its posterior deployment.

Language: HTML - Size: 9.7 MB - Last synced at: 10 days ago - Pushed at: over 6 years ago - Stars: 9 - Forks: 1

angelovangel/nxf-fastqc

A simple fastp-MultiQC nextflow pipeline

Language: Nextflow - Size: 36.5 MB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 5 - Forks: 3

dolphinnext/rnaseq Fork of onuryukselen/rnaseq

RNA-Seq pipeline

Language: Nextflow - Size: 31.8 MB - Last synced at: over 2 years ago - Pushed at: almost 3 years ago - Stars: 3 - Forks: 5

wanyuac/ARIBA_toolkit

Scripts for ARIBA-based gene detection

Language: Python - Size: 34.2 KB - Last synced at: over 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 1

SCC-LZU/LGAflow

A Genome Annotation workflow for Eukaryotes

Language: Nextflow - Size: 29.6 MB - Last synced at: almost 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 3

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

jtorrex/nextflow-test-pipelines

Testing different pipelines using Nextflow

Language: C++ - Size: 3.06 MB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

angelovangel/nxf-dada2

A nextflow pipeline for the analysis of 16S amplicon data built around RExMap

Language: R - Size: 132 KB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

biodata-fun/nf_genomics_pipelines

This repo contains pipeline implemented using the nextflow workflow management system for the analysis of genomics data

Language: Nextflow - Size: 72.3 KB - Last synced at: over 2 years ago - Pushed at: almost 4 years ago - Stars: 2 - Forks: 1

eipm/hello-nextflow

An hello world pipeline to test nextflow installations.

Language: Nextflow - Size: 265 KB - Last synced at: over 2 years ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0

dolphinnext/chipseq Fork of onuryukselen/chipseq

Chip-Seq pipeline

Language: Nextflow - Size: 21.7 MB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 4

biodata-fun/course_material

This directory contains material that I've used in different courses

Size: 2.92 MB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

dolphinnext/atacseq Fork of onuryukselen/atacseq

Atac-Seq pipeline

Language: Nextflow - Size: 7.62 MB - Last synced at: over 2 years ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 2

csawye01/nf-core-demultiplex

Demultiplexing pipeline for sequencing data

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