All Published Workflows

7 workflows that have been reviewed and published

pcr_product_anl
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pcr_product_anl
public

public

''' snakemake --cores 10 --snakefile /TBI/Share/BioPeople/siyoo/Pipelines/customppl_anlbio_motif/workflow/Snakefile --configf...
Protein sequence analysis Snakemake Protein expression
Free
10
automated-functional-annotation-using-snakemake
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Snakemake workflow for functional annotation using eggNOG mapper v2
public

public

Snakemake workflow for automated functional annotation This is a Snakemake workflow for performing functional annotation o...
Annotation track Gene functional annotation Report Diamond Snakemake Protein expression
Free
1
ddamsproteomics
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Quantitative shotgun MS proteomics
public

public

Quantitative shotgun MS proteomics as done in Lehtio lab The pipeline is built using Nextflow , a workflow...
msgf_plus Spectra Nextflow OpenMS Quant Protein expression Protein interactions Protein structure analysis
Free
22
ejp-rd-wp13-case-study-cakut-proteome-peptidome-an
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EJP-RD WP13 case-study: CAKUT proteome, peptidome and miRNome data analysis using WikiPathways
public

public

In this analysis, we created an extended pathway, using the WikiPathways repository (Version 20210110) and the three -omics...
Snakemake WorkflowHub Protein expression Protein structure analysis Proteomics
Free
1
ejp-rd-wp13-case-study-cakut-peptidome-and-mirnome
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EJP-RD WP13 case-study: CAKUT peptidome and miRNome data analysis using the DIABLO and PLS-DA methods from the mixOmics R package
public

public

For integrative analysis of CAKUT multi-omics data DIABLO method of the mixOmics package (version 6.10.9. Singh et. al. 201...
Snakemake WorkflowHub Protein expression Proteomics
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
nf-core-circrna
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circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
public

public

nf-core/circrna is a best-practice analysis pipeline for the quantification, miRNA target prediction and differential expr...
circexplorer2 ciriquant dcc miranda BEDTools Bowtie 2 BWA DESeq2 FastQC gtftogenepred HISAT2 MapSplice MultiQC Nextflow pheatmap SAMtools STAR StringTie ggplot2 Trim_Galore Function analysis Protein expression
Free
71