All Published Workflows
277 workflows that have been reviewed and published
Near-real time tracking of SARS-CoV-2 in Connecticut
Repository containing scripts to perform near-real time tracking of SARS-CoV-2 in Connecticut using genomic data. This pipeli...
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...
Snakemake pipelines for nanopore sequencing data archiving and processing
Detailed documentation and tutorials are available at readthedocs . Nanopype is a snakemake based pipeline providing conv...
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
A Snakemake workflow to run and benchmark structure learning (a.k.a. causal discovery) algorithms for probabilistic graphical models.
Benchpress [1] is a Snakemake workflow where structure learning algorithms, implemented in possibly different lang...
Amplicon sequence processing workflow using QIIME 2 and Snakemake
Tourmaline is an amplicon sequence processing workflow for Illumina sequence data that uses QIIME 2 and the software pack...
Use an ensemble of variant callers to call variants from ATAC-seq data
A pipeline for running an ensemble of variant callers to predict variants from ATAC-seq reads. The entire pipeline is made up...
Integrated workflow for SV calling from single-cell Strand-seq data
Structural variant calling from single-cell Strand-seq data Snakemake pipeline. This workflow uses Snakemake to
execu...
mosaicatcher
tabix
BCFtools
BEDTools
ComplexHeatmap
Pandas
pheatmap
SAMtools
Snakemake
TensorFlow
WhatsHap
assertthat
BiocManager
cowplot
data.table
devtools
dplyr
ggnewscale
ggplot2
ggpubr
matrixStats
optparse
RColorBrewer
reshape
reshape2
scales
stringr
tibble
tidyr
intervaltree
matplotlib
numpy
parmap
plotly
pysam
PyYAML
scipy
seaborn
tqdm
xopen
StaG Metagenomic Workflow Collaboration
The StaG Metagenomic Workflow Collaboration (mwc) project focuses on providing
a metagenomics analysis workflow suitable for ...
Reproducible workflow for SARS-CoV-2 recombinant sequence detection.
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Note : ncov-recombinant will be deprecated soon as SARS-CoV-2 recombination has evolved beyond the scope of this pip...
Sparse Signaling Pathway Sampling: MCMC for signaling pathway inference
Code related to the manuscript
Inferring signaling pathways with probabilistic programming
(Merrell & Gitter, 2020) B...
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