snakemake-workflow

There are 1 repository under snakemake-workflow topic.

• 4dn-dcic / tibanna

  Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.

  pipelinesaws-step-functionawsdockeraws-lambdabioinformaticscwlwdlcwl-workflowwdl-workflowsnakemakesnakemake-workflowconda
  Language:Python 69

• felixleopoldo / benchpress

  A Snakemake workflow to run and benchmark structure learning (a.k.a. causal discovery) algorithms for probabilistic graphical models.

  graphical-modelsbayesian-networksmarkov-networksbenchmarkingreproducible-researchmachine-learningsnakemake-workflowstructure-learningcausal-discoverycausal-modelscausality
  Language:Python 61

• lachlandeer / snakemake-econ-r

  reproducible research project template for R using Renv and snakemake with an econ application

  snakemakesnakemake-workfloweconomicsworkflowrenvreproducible-researchreproducibility
  Language:R 61

• centrefornetzero / pypsa-fes

  A model that optimises investment and operation, and incorporates flexibility domestic demand flexibility to model scenarios for Great Britain's future energy system.

  energyenergy-transitiongreat-britainmodellingopen-sourceoptimizationpythonsector-couplingsnakemake-workflowdemand-flexibilityenergy-modelenergy-system-modelpower-systemspypsa
  Language:Python 20

• laelbarlow / amoebae

  Workflow for identifying and classifying homologous gene/protein sequences

  bioinformaticshmmer3biopythonpython3blastgenome-annotationsimilarity-searchcoulson-plottranscriptome-annotationsnakemake-workflowcomparative-genomicshomologymolecular-evolutiongene-familiesprotein-familiesorthology
  Language:Python 20

• sanjaynagi / rna-seq-pop

  Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data

  snakemake-workflowrna-seqvariant-callingdifferential-expressionpopulation-genomicssnakemaketranscriptomicsworkflowpopulation-geneticsselectionkaryotypeancestrygenomic-surveillance
  Language:Jupyter Notebook 17

• NovembreLab / eems-around-the-world

  Repo to analyze population genetic data with many different methods

  population-geneticsdata-visualizationprinciple-component-analysisstructureadmixturesnakemake-workflow
  Language:R 15

• s-shemmee / s-shemmee

  Config files for my GitHub profile.

  githubreadmereadme-actionreadme-badgesreadme-banner-generatorreadme-cardreadme-editsreadme-generatorreadme-mdreadme-profilereadme-statsreadme-templategithub-readme-profilegithub-actionsgithub-statssnakemake-workflow
  15

• metagenlab / MeSS

  Snakemake pipeline for simulating shotgun metagenomic samples

  bioinformaticsshotgun-metagenomicssnakemake-workflow
  Language:Python 14

• guigolab / LyRic

  Long RNA-seq analysis workflow

  bioinformaticsclsgencodepacbio-iso-seqrnaseqsnakemake-workflowtranscriptomics
  Language:Python 10

• ylab-hi / ScanNeo2

  Snakemake-based computational workflow for neoantigen prediction from diverse sources

  epitopegene-fusionindelsneoantigenspeptidesnakemakesnakemake-workflowsplicingexitronneoepitope
  Language:Python 8

• svsuresh / salmon_deseq2_snakemake

  This repository has snakemake scripts for salmon-deseq2 pipeline for RNAseq data analysis

  salmon-deseq2snakemake-workflow
  Language:R 7

• dohlee / snakemake-hamburger

  :snake::hamburger: A beginner's guide to modular snakemake workflows.

  snakemakesnakemake-workflowreproducible-researchbioinformatics-pipeline
  Language:Python 6

• fritzbayer / snakemake-with-R

  Simple template for running snakemake with R

  r-workflowsnakemakesnakemake-pipelinesnakemake-workflow
  Language:R 6

• mjmlab / pyinseq

  Python pipeline for analyzing INSeq Insertion Sequencing data

  inseqtn-seqsnakemake-workflowgenbank-files
  Language:Python 6

• RIVM-bioinformatics / SARS2seq

  SARS2seq is a pipeline designed to process raw FastQ data from targeted SARS-CoV-2 sequencing and generate biologically correct consensus sequences of the SARS-CoV-2 genome.

  coronaviruscoronavirus-analysisrivmbioinformaticsvirologyvirusespublic-healthsnakemakesnakemake-workflowconsensus-sequencespythonngs-analysis
  Language:Python 6

• vibaotram / baseDmux

  snakemake workflow for basecalling and demultiplexing of ONT sequencing data

  snakemake-workflowbasecallingdemultiplexingnanopore
  Language:Python 6

• allytrope / variant-analysis

  A Snakemake pipeline for variant calling of genomic FASTQ data using GATK

  bioinformatics-workflowbioinformaticsvariant-callingsnakemake-workflow
  Language:Python 5

• pyc1216 / hlaloh-pipeline

  hla-typing by optitype & polysolver , detect loh by lohhla.

  snakemake-workflowdocker-imagehla-typing
  Language:R 5

• RIVM-bioinformatics / ViroConstrictor

  ViroConstrictor is a pipeline designed to process raw FastQ data from viral amplicon-based sequencing and generate biologically correct consensus sequences of the given viral genome

  pythonbioinformaticssnakemakevirusespublic-healthvirologyngs-analysissnakemake-workflowrivmconsensus-sequencesanalysis
  Language:Python 5

• Serka-M / mmlong2-lite

  Lightweight bioinformatics pipeline for microbial genome recovery

  bioinformaticslong-read-sequencingmetagenome-assembled-genomesmetagenomicsmicrobial-genomicsmicrobiomenanoporepacbiosingularity-containersnakemake-workflow
  Language:Python 5

• chazeon / dpgen-snakemake

  A lightweight Snakemake-based workflow that implements the DP-GEN scheme.

  workflowsnakemake-workflowmachine-learning-potentialab-initiodeep-learning
  Language:Python 4

• deepalivasoya / Snakemake-food

  snakemakesnakemake-pipelinessnakemake-workflowfoodrecipes
  Language:Python 4

• niekwit / rna-seq-salmon-deseq2

  Snakemake workflow for RNA-Seq differential transcript analysis using Salmon/Deseq2

  bioinformaticssnakemakesnakemake-workflow
  Language:Python 4

• thomasbtf / document-anonymization

  Personal data redaction on images based on FHIR patient resources.

  documentpseudonymizationfhirsnakemake-workflow
  Language:Python 4

• weigelworld / auto-asm

  snakemake long read assembly pipeline

  bioinformaticsgenome-assemblybioinformatics-pipelinesnakemake-workflow
  Language:Python 4

• emleddin / md-analysis-workflow

  A Snakemake workflow for analyzing AMBER molecular dynamics simulations.

  snakemake-workflowmolecular-dynamicsreproducible-researchamber
  Language:Python 3

• fungenomics / scCoAnnotate

  Pipeline for consensus prediction of cell types in single-cell RNA sequencing data.

  cell-type-classificationreproducible-researchsingle-cellsingle-cell-rna-seqsnakemake-workflow
  Language:R 3

• hivlab / ena-upload

  Snakemake workflow to upload Sars-Cov-2 reads to ENA

  snakemake-workflowsars-cov-2korogeno-estcovid-19-estoniasnakemakesnakefileuploadena
  Language:Python 3

• insilicoconsulting / snake-chic

  Snakemake wrapper around the Arima Capture Hi-C (CHiC) workflow

  bioinformaticsgenomicshi-chicsnakemakesnakemake-workflowworkflow
  Language:Python 3

• niekwit / crispr-screens

  Snakemake workflow for CRISPR-Cas9 screen analysis

  bioinformatics-pipelinecrispr-screen-analysissnakemake-workflow
  Language:Python 3

• niekwit / cut_and_run

  Snakemake workflow for Cut & Run

  bioinformaticsngs-analysissnakemakesnakemake-workflow
  Language:Python 3

• niekwit / damid-seq

  Snakemake workflow for DamID-Seq analysis

  bioinformatics-pipelinedamidsnakemake-workflow
  Language:Python 3

• niekwit / rna-seq-star-tetranscripts

  Snakemake workflow for transposable element RNA-Seq using TEtranscripts

  ngs-pipelinerna-seq-pipelinesnakemake-workflowtransposable-elements
  Language:R 3

• zavolanlab / SCUREL

  Method to detect 3'UTR changes from scRNA-seq

  scrnaseqbioinformaticssnakemake-workflow
  Language:Python 3

• Zhanglab-IOZ / TnpB

  Snakemake workflows for TAM depletion analysis and de novo IS605 annotation

  insertion-sequencessequencingsnakemake-workflow
  Language:Python 3