All Published Workflows
225 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 ...
![armor](https://media.bioworkflows.com/bioworkflows/public_preview/cc7665c55e38e46bd0aba5fbf5b6c09f9be831437a05f091d0e4ec7b56ab42a9.jpg)
Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data
ARMOR ( A utomated R eproducible MO dular R NA-seq) is a Snakemake workflow , aimed at performing a ty...
![dropseqpipe](https://media.bioworkflows.com/bioworkflows/public_preview/eb7fcd8e1164cad84e7e17d081078dfde291fa5783b495a811a77d95a2fd4bf5.jpg)
A SingleCell RNASeq pre-processing snakemake workflow
This pipeline is based on snakemake and the dropseq tools provided by the McCarroll Lab . It allows to go from raw da...
![dna-seq-varlociraptor](https://media.bioworkflows.com/bioworkflows/public_preview/d340f005ebb434d0f6a6cb675215dd3df9d4a4e20a9e384a028fcb5cfcf3209d.jpg)
A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of Varlociraptor.
A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse...
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raw sequence reads
Variant calling
genetic variants
delly
gatk
rust-bio-tools
snakemake-wrapper-utils
tabix
BCFtools
BEDTools
Bowtie 2
BWA
Cutadapt
FastQC
fgbio
FreeBayes
mosdepth
MultiQC
Pandas
Picard
SAMtools
Snakemake
Variant Effect Predictor (VEP)
vembrane
numpy
oschmod
sklearn
statsmodels
Varlociraptor
DNA
![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
![natrix](https://media.bioworkflows.com/bioworkflows/public_preview/e869c6522fdc626f4352051ec23940335655df117c2d7043aaa2d8b10f40a115.jpg)
Open-source bioinformatics pipeline for the preprocessing of raw sequencing data.
Natrix is an open-source bioinformatics pipeline for the preprocessing of raw sequencing data.
The need for a scalable, repro...
![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...
![dna-seq-neoantigen-prediction](https://media.bioworkflows.com/bioworkflows/public_preview/567dd1c7d8df937875297f21b13a6921a21676de385d24ca874095af9ddecec1.jpg)
Neoantigen Prediction Snakemake Workflow: Genomic Variant Detection and Peptidome Incorporation
This workflow detects genomic variants with Strelka and and tries to incorporate germline and somatic variants into a sam...
Sequence
Genetic variation analysis
genetic variants
gatk
hla-la
rust-bio-tools
tabix
Arriba
BCFtools
BWA
Cutadapt
FreeBayes
kallisto
Microphaser
NetMHCIIpan
NetMHCpan
Pandas
Picard
Quant
razers3
SAMtools
Snakemake
STAR
Strelka
Variant Effect Predictor (VEP)
vembrane
Jinja2
numpy
Varlociraptor
Genomics
![nbis-meta](https://media.bioworkflows.com/bioworkflows/public_preview/a313d869a5ece3cb72c146dd91f5ddf1cba1017dc12325245ea497335fce687c.jpg)
A snakemake workflow for metagenomic projects
A workflow for metagenomic projects A snakemake workflow for
paired- and/or single-end whole-genome shotgun metagenomic d...
Barrnap
prodigal
MEGAHIT
Biopython
BLAST
Bowtie 2
Centrifuge
CheckM
contigtax
Cutadapt
edgeR
eggNOG-mapper v2
FastANI
FastQC
FeatureCounts
Infernal cmscan (EBI)
kraken2
Krona
MaxBin
MetaBAT 2
metagenomeSeq
MetaPhlAn
metaspades
MultiQC
Pandas
Picard
SAMtools
seqtk
Snakemake
SortMeRNA
SqueezeMeta
Trimmomatic
Trnascan-SE
CONCOCT
common
gtdbtk
networkx
numpy
RGI
![ameta](https://media.bioworkflows.com/bioworkflows/public_preview/69dd01137d0ae012a95788d05e91437b4d97f42b53a32a7ca5c8098cebd5dedf.jpg)
![cascabel](https://media.bioworkflows.com/bioworkflows/public_preview/a2df8d8c46e7dad17f372775df60aaf13d4ed5a4b9ccefb69264ffd46c8857b5.jpg)
![pacman-pipeline](https://media.bioworkflows.com/bioworkflows/public_preview/c0d52259b3a96514e06006619903f013a8f42cc264249e87a7b8fe9beb1a65a3.jpg)
Bioinformatics pipeline for the analysis of amplicon sequencing data of eDNA samples from the PacMAN project
This is the bioinformatics pipeline developed for the PacMAN (Pacific Islands Marine Bioinvasions Alert Network). This pipeli...