All Published Workflows

6 workflows that have been reviewed and published

rna-seq-kallisto-sleuth
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A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
public

public

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth . The usage of thi...
JSON Expression data Expression analysis Expression data bioawk snakemake-wrapper-utils biomaRt IHW Biopython BWA CPAT Cutadapt fgsea graphite GSEA IsoformSwitchAnalyzeR kallisto limma Pandas pheatmap Picard Quant SAMtools sleuth Snakemake SPIA dplyr fs ggplot2 ggpubr gridExtra tidyr tidyverse altair altair-saver goatools matplotlib numpy pysam scipy RNA-Seq
Free
105
pyflow-atacseq
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ATAC-seq snakemake pipeline
public

public

source: http://www.the-scientist.com/?articles.view/articleNo/44772/title/Reveling-in-the-Revealed/ https://www.biostars.org/...
Expression data Peak calling Plot macs2 ataqv BEDTools Bowtie 2 DeepTools FastQC MultiQC SAMBLASTER SAMtools Snakemake ATAC-seq
Free
16
hull_microbiome_cluster_workflow
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Snakemake workflow for microbiome research cluster analysis using fastp, Kraken2, and BIOM.
public

public

A Snakemake workflow to analyse long read human microbiome data with steps for general quality control and taxonomy assignmen...
Expression data Sequencing quality control Taxonomy kraken-biom fastp kraken2 seqkit Snakemake Taxonomy
Free
8
gps_paper_pipeline
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Pipeline for the manuscript 'Accurate detection of shared genetic architecture from GWAS summary statistics in the small-sample context'
public

public

This repository contains a snakemake pipeline for the reproduction of the results in the manuscript named above. The file...
Expression data Modelling and simulation Molecular simulation data plink2 Pandas patcHwork pLink Snakemake argparse data.table evd fitdistrplus ggplot2 ggpubr Hmisc magrittr mvtnorm Rcpp scales stringr numpy scipy simGWAS Genetics
Free
170
cosifer-1
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COSIFER-COnSensus Interaction Network InFErence Service
public

public

Inference framework for reconstructing networks using a consensus approach between multiple methods and data sources. Manica...
Expression data Correlation Matrix COSIFER Molecular genetics
Free
1
cosifer
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COSIFER - COnSensus Interaction Network InFErence Pipeline
public

public

Inference framework for reconstructing networks using a consensus approach between multiple methods and data sources. Manica...
Expression data Regression analysis ID list COSIFER Molecular genetics
Free
1