All Published Workflows
109 workflows that have been reviewed and published
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...
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
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
Workflow for Nanopore Sequencing of 10x single cell libraries
ScNapBar (single-cell Nanopore barcode demultiplexer) is a workflow to assign barcodes to long-read single-cell sequencing...
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
Cell cycle analysis of single-cell proteomic and transcriptomic data for the FUCCI cell model
This repository contains the code used to perform the single-cell proteogenomic analysis of the human cell cycle . This s...
A Snakemake workflow for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, and GSEApy.
Given human (hg19 or hg38) or mouse (mm9 or mm10) based genomic region sets (i.e., region sets) and/or (ranked) gene sets...
kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.
A modular, flexible, and reproducible Snakemake workflow to perform k-mers-based GWAS.
Summary
Installation
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Clin-mNGS: Automated pipeline for pathogen detection from clinical metagenomic data
The Clin-mNGS pipeline is an integrated, open-source, scalable, reproducible, and user-friendly framework scripted using the ...
Genome Assembly Validation via Inter-SUNK distances in ONT reads
Genome Assembly Validation via Inter-SUNK distances in nanopore reads Setup source files in config.yaml and ont.tsv config.ya...
Metagenomic-metabolomic associations workflow
This workflow is designed to study large arrays of multiomics data by analyzing patterns of cooccurrence
of pairs of metageno...
