All Published Workflows

11 workflows that have been reviewed and published

gtex-gatk4
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GATK4 Pipeline for GTEx Somatic Mutation Analysis
public

public

Snakemake implementation of GATK4 pipeline for GTEx Project A collection of subworkflows to manage the analysis and variant ...
Snakemake DNA mutation
Free
1
hyperpanel
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Hypermutated Tumor Mutational Signature Detection and Visualization Pipeline
public

public

This pipeline is designed to detect and visualise Mutational Signatures in Hypermutated Tumors Designed and Edited by : Moham...
Snakemake snpEff SnpSift matplotlib PIL PyVCF DNA mutation
Free
14
synonymous_nonysynonymous
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A snakemake workflow for analysing synonymous and nonsynonymous mutations
public

public

This simple workflow constructs RSV-A and RSV-B synonymous and nonsynonymous mutation graphs. These graphs are scaled by gene...
JSON Gene tree Sequence mutation and randomisation Plot Biopython Pandas Snakemake matplotlib numpy DNA mutation
Free
2
rnadnavar
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Pipeline for RNA and DNA integrated analysis for somatic mutation detection
public

public

Hi beta-tester, thanks for agreeing to help out in this repo. I have created a project to add issues/tasks. Plese feel fr...
Variant filtering biopet-vcffilter gatk manta tabix dragmap BCFtools BWA Bwa-mem2 fastp FastQC FreeBayes HISAT2 mosdepth MultiQC Nextflow SAMtools STAR Strelka Variant Effect Predictor (VEP) VCFtools vt DNA DNA mutation RNA
Free
13
trio-analysis
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Trio Analysis with the use of the HTSGET protocol
public

public

To discover causal mutations of inherited diseases it’s common practice to do a trio analysis. In a trio analysis DNA is sequ...
python-htsget BCFtools EGA Galaxy GEMINI Iobio snpEff WorkflowHub DNA mutation Whole genome sequencing
Free
python-mutation-free-energy-calculations-using-bio
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Python Mutation Free Energy Calculations using BioExcel Building Blocks (biobb)
public

public

Mutation Free Energy Calculations using BioExcel Building Blocks (biobb) Based on the official pmx tutorial . This tu...
biobb_common biobb_gromacs biobb_pmx Gromacs biobb-analysis biobb-common biobb-gromacs biobb-pmx DNA mutation Protein interactions
Free
1
python-protein-md-setup-tutorial-with-mutations
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Python Protein MD Setup tutorial with mutations using BioExcel Building Blocks (biobb)
public

public

Based on the official GROMACS tutorial . This tutorial aims to illustrate the process of setting up a simulation system c...
biobb_structure_utils biobb_analysis biobb_chemistry biobb_common biobb_gromacs biobb_model genion Gromacs editconf biobb-analysis biobb-common biobb-gromacs biobb-model biobb-structure-utils DNA mutation Protein expression
Free
1
cwl-protein-md-setup-tutorial-with-mutations
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CWL Mutations Protein MD Setup tutorial using BioExcel Building Blocks (biobb)
public

public

Based on the official GROMACS tutorial . This tutorial aims to illustrate the process of setting up a simulation system c...
CWL biobb_structure_utils biobb_analysis biobb_chemistry biobb_gromacs biobb_model genion Gromacs editconf gmx energy DNA mutation Protein interactions
Free
17
jupyter-notebook-mutation-free-energy-calculations
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Jupyter Notebook Mutation Free Energy Calculations using BioExcel Building Blocks (biobb)
public

public

Mutation Free Energy Calculations using BioExcel Building Blocks (biobb) Based on the official pmx tutorial . This tu...
Calculation Genome analysis biobb_analysis biobb_gromacs biobb_pmx Gromacs gmx energy biobb-analysis biobb-gromacs biobb-pmx ipython plotly DNA mutation
Free
21
covid-19-varscan
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COVID-19: Detecting SNPs and INDELs using VARSCAN
public

public

Detects SNPs and INDELs using VARSCAN2. This workflow is about Covid-19.
Bowtie 2 BWA fastp Galaxy MultiQC SAMtools SRA Software Toolkit VarScan Vcflib WorkflowHub DNA mutation
Free
covid-19-gatk4
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COVID-19: Detecting SNPs and INDELs using GATK4
public

public

Detects SNPs and INDELs. This workflow is about Covid-19.
gatk4 Bowtie 2 BWA fastp Galaxy MultiQC SAMtools snpEff SRA Software Toolkit Vcflib WorkflowHub DNA mutation
Free