All Published Workflows
183 workflows that have been reviewed and published
![rna-seq-star-deseq2](https://media.bioworkflows.com/bioworkflows/public_preview/2b57d357da619c31943bbffc57e2cc955325669933c9b5b91e33b81fd78c18d4.jpg)
RNA-seq workflow using STAR and DESeq2
This workflow performs a differential gene expression analysis with STAR and Deseq2. The usage of this workflow is described ...
![single-cell-rna-seq](https://media.bioworkflows.com/bioworkflows/public_preview/c306f1cae484b82a70590e0991c7f26d5b60a8afff206f0c119cc00415d05d70.jpg)
A single cell RNA-seq workflow, including highly variable gene analysis, cell type assignment and differential expression analysis.
A single cell RNA-seq workflow following Lun, McCarthy and Marioni 2016 and Soneson and Robinson 2018 , with added mo...
![rna-seq-kallisto-sleuth](https://media.bioworkflows.com/bioworkflows/public_preview/76a6f39480d6ade510201e74d885f132220f55b66883fb76d168379b3cb3bbfd.jpg)
A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth . The usage of thi...
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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
![score-assemblies](https://media.bioworkflows.com/bioworkflows/public_preview/d00200dfb7483e04ff9df2ae8ccf321113edce92a30cf20ff777932747cc26f1.jpg)
Score and compare multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s)
A snakemake-wrapper for evaluating de novo bacterial genome assemblies, e.g. from Oxford Nanopore (ONT) or Illumina seque...
![chipseq](https://media.bioworkflows.com/bioworkflows/public_preview/d5a1471bc769b0779a03b6e92fa2cd39daf943eed9df28474a728f4f3f6602cb.jpg)
ChIP-seq peak-calling, QC and differential analysis pipeline (Snakemake port of the nextflow pipeline at https://nf-co.re/chipseq).
This is the template for a new Snakemake workflow. Replace this text with a comprehensive description covering the purpose an...
![haplotyped-methylome](https://media.bioworkflows.com/bioworkflows/public_preview/c1ff349f0272be2119a2caa85dba16084ec820120f1cd835a8a7c3a68dfb8320.jpg)
Reproducibility workflow for Gigante et al., 2018: Using long-read sequencing to detect imprinted DNA methylation
Reproducibility instructions for Gigante et al., 2019.
Note: this repository is still being tested! If you find a bug, plea...
![rna-seq-pop](https://media.bioworkflows.com/bioworkflows/public_preview/8072e368f6deef82a6e087d8d748ef74fe8cacbf83d53b8c5ca7e9191e8815a0.jpg)
Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data
Documentation : https://sanjaynagi.github.io/rna-seq-pop/
Walkthrough : https://www.youtube.com/watch?v=5QQe7DLHO4...
FASTQ-illumina
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Sample annotation
Variant calling
genetic variants
snakemake-wrapper-utils
EnhancedVolcano
BCFtools
DESeq2
fastp
FreeBayes
GLUE
HISAT2
kallisto
mosdepth
MultiQC
Pandas
pheatmap
Quant
SAMBLASTER
SAMtools
sleuth
Snakemake
snpEff
Vcflib
data.table
dplyr
ggplot2
ggrepel
jsonlite
openxlsx
RColorBrewer
tidyverse
ipykernel
matplotlib
matplotlib-venn
numpy
papermill
pop-tools
scipy
zarr
Population genomics
![pyflow-scatacseq](https://media.bioworkflows.com/bioworkflows/public_preview/a360df3bc85b86f650820edbe03976da1d8bd91d03f3a54f9d714760103e7f86.jpg)
![mikropml-snakemake-workflow](https://media.bioworkflows.com/bioworkflows/public_preview/041d6161bc4b407e0ea37d87f33bdf0531c4e31e283f0f52a3fd583e9e6e4550.jpg)
Snakemake template for building reusable and scalable machine learning pipelines with mikropml
Snakemake is a workflow manager
that enables massively parallel and reproducible
analyses.
Snakemake is a suitable tool to...
![cuttag-pipeline](https://media.bioworkflows.com/bioworkflows/public_preview/07a6935d8d1643b03df56b67ca4018640c79988e4375325b5496367fcf47a888.jpg)
Pipeline for Cut&Tag analysis
Snakemake pipeline for Cut&Tag analysis
# cd into a project directory
# type the following to get a copy of the pipeline
git ...
![tapseq_manuscript](https://media.bioworkflows.com/bioworkflows/public_preview/aeeb1fce3233427d6d70986f34812d798674901dc3b6fc6d8acc7a80ee611223.jpg)
Analysis code for the TAP-seq manuscript.
This repository contains code to reproduce the results presented in the article. It builds upon a snakemake workflow that...
bigWig
ucsc-liftover
BiocParallel
Biopython
Biostrings
BSgenome
Consensus
GenomicAlignments
GenomicFeatures
GenomicRanges
HiTC
Pandas
Picard
rtracklayer
SAMtools
Snakemake
STAR
Trimmomatic
corrplot
eulerr
factoextra
GGally
ggplot2
ggpubr
ggrepel
gridExtra
here
kableExtra
Matrix
optparse
plotly
pROC
readxl
tidyverse
numpy
plotly
![bo-demography](https://media.bioworkflows.com/bioworkflows/public_preview/ebaad6be60a2cfbd7e3eba5cc147b7d423f34110178ca07c9c11b6bc1ac9135b.jpg)
Demographic analysis of Brassica oleracea
Demographic analysis of Brassica oleracea Follows GATK4 best practices (https://software.broadinstitute.org/gatk/best-practic...