All Published Workflows
353 workflows that have been reviewed and published
![psychip_snakemake](https://media.bioworkflows.com/bioworkflows/public_preview/791b56ccab3630bcb1746d66097f813640394655ed21d3c39cb591b7016d2994.jpg)
ENCODE pipeline for histone marks developed for the psychENCODE project
psychip pipeline is an improved version of the ENCODE pipeline for histone marks developed for the psychENCODE project.
The o...
![cellranger-snakemake-gke](https://media.bioworkflows.com/bioworkflows/public_preview/1045115046015ac39a849801172555df3b41ec5023f7f7c8230f0640b8f89a2b.jpg)
snakemake workflow to run cellranger on a given bucket using gke.
A Snakemake workflow for running cellranger on a given bucket using Google Kubernetes Engine. The usage of this workflow ...
![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 ...
![dna-seq-gatk-variant-calling](https://media.bioworkflows.com/bioworkflows/public_preview/4b8eed0f6a179f18a43e601e653aee298718468aaf37ee1b3d0f8dddaffcaf6a.jpg)
This Snakemake pipeline implements the GATK best-practices workflow
This Snakemake pipeline implements the GATK best-practices workflow for calling small germline variants. The usage of thi...
![metagem](https://media.bioworkflows.com/bioworkflows/public_preview/9f897d1e5c5be9ea5b04501012110b7aa72e59b8354584eea77e29aa4202b7ae.jpg)
:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
Note An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic inte...
![v-pipe](https://media.bioworkflows.com/bioworkflows/public_preview/711074687ab0ba435f238465ae19915ac94bb8a0078e32ad735c3188c812096d.jpg)
V-pipe is a pipeline designed for analysing NGS data of short viral genomes
V-pipe is a workflow designed for the analysis of next generation sequencing (NGS) data from viral pathogens. It produces a n...
![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
![stainedglass](https://media.bioworkflows.com/bioworkflows/public_preview/806d018c3cb232f52b73e59ded90b880e1dde535430b4937b7c55abda2eade05.jpg)
Make colorful identity heatmaps of genomic sequence
This is a repository for making colorful identity heatmaps of genomic sequence. To install you can follow the directions on t...
![lathe](https://media.bioworkflows.com/bioworkflows/public_preview/1f180f3eaf10aa1f49825688bd4634606b3e4c92a2d6c655dd34486bf7715039.jpg)
A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
A tool for generating bacterial genomes from metagenomes with Nanopore long read sequencing First, install miniconda3 The...
![covid-19-signal](https://media.bioworkflows.com/bioworkflows/public_preview/654963db437af051ec1197e3ab2a3eb4c6cbdc09928cdc2b32ea2aa3d58d2787.jpg)
Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
This is a complete standardized workflow the assembly and subsequent analysis for short-read viral sequencing.
This core work...
![pore-c-snakemake](https://media.bioworkflows.com/bioworkflows/public_preview/e54f914fc5d5149995f5a7f75fd228a68ea734356972cfeb176e1da9d6c31022.jpg)
Pore-C Snakemake Workflow for Processing and Analysis of Nanopore Sequencing Data
This pipeline manages a pore-c workflow starting from raw fastq files and converting them to standard file formats for use by...