All Published Workflows

9 workflows that have been reviewed and published

armor
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Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data
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ARMOR ( A utomated R eproducible MO dular R NA-seq) is a Snakemake workflow , aimed at performing a ty...
JSON User metadata Expression analysis Quality control report bedGraphToBigWig BEDTools Cutadapt FastQC MultiQC Quant Salmon SAMtools Snakemake STAR Trim_Galore RNA-Seq
Free
22
rna-seq-kallisto-sleuth
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A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
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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
rnaseq
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RNAseq Differential Expression Analysis Workflow with STAR and DESeq2
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public

This workflow performs a differential expression analysis using STAR and DESeq2 . It performs a wide range of quality...
Expression analysis PCAtools AnnotationHub BiocParallel Cutadapt DESeq2 GFFutils limma MultiQC Pandas Snakemake STAR cowplot ggplot2 ggrepel tidyverse RNA-Seq
Free
22
simple-snakemake-secondary-workflow
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Demo Snakemake workflow - small and runs quickly for testing purposes.
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public

Small demo workflow following best practice template for Snakemake workflows . Just includes bowtie2, fastqc and trim_gal...
raw sequence reads Expression analysis Report Bowtie 2 FastQC SAMtools Snakemake Trim_Galore Genomics
Free
5
snakemake-salmon
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RNA-Seq Data Analysis Workflow using Snakemake and Salmon for Gene Expression Quantification and Differential Expression Analysis
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A simple Snakemake workflow for processing RNA-Seq using snakemake in conjunction with salmon . Data is assumed to be p...
Expression analysis Quantification AdapterRemoval FastQC Quant Salmon SAMtools Snakemake Gene expression
Free
21
2022-rnaseq-cloud
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RNA-Seq in the Cloud
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public

June 21 & 23, 2021 CFDE Workshop Open access Requires github login Adapted for CFDE workshop from materials developed by Tayl...
FASTQ raw sequence reads Expression analysis Quality control report FastQC MultiQC Quant Salmon Snakemake Trimmomatic RNA-Seq
Free
9
snakemake_rnaseq_preprocess_pipeline
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RNA-seq Preprocessing Pipeline with Snakemake for Differential Expression Analysis
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public

Basic snakemake workflow for preprocessing the bulk RNAseq data from fastq files to counts table which can be used as an inpu...
Expression analysis fastp FastQC FeatureCounts MultiQC Snakemake STAR RNA-Seq
Free
6
analysis_of_multi_way_chromatin_interactions_from_
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Analysis of multi-way chromatin interactions from very long sequencing reads
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public

The thesis is focused on the concept of “chromosomal walks” introduced by Olivares-Chauvet et al., 2016. These chromosomal wa...
TSV paired sequencing data Expression analysis Filtering Plot BEDTools Biopython Bowtie 2 Pandas SAMtools Snakemake intervaltree matplotlib networkx numpy pysam scipy seaborn De Novo
Free
17
bgnn_core_workflow
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First complet version of the workflow with snakemake
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public

First complete version of the BGNN image segmentation workflow managed using snakemake. The image segmentation workflow is ma...
Image Expression analysis Ontology metadata segmentation-fold Snakemake morphology analysis
Free
5