All Published Workflows
269 workflows that have been reviewed and published
![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...
![pipeline-transcriptome-de](https://media.bioworkflows.com/bioworkflows/public_preview/602f5af232359582918564dd5a4f011be7be53b91e1b71369ede3cf7221c6120.jpg)
Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
This project is deprecated. Please see our newer wf-transcriptomes , which contains functionality for differential exp...
![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
![kraken2_classification](https://media.bioworkflows.com/bioworkflows/public_preview/7a6a1fc5df6f57a31b800266881003949ffd206a1fb736004fc09825dfc9ba7d.jpg)
Snakemake workflow for metagenomic classification with Kraken2
A Snakemake pipeline wrapper of the Kraken2 short read metagenomic classification software, with additional tools for analysi...
![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...
![varca](https://media.bioworkflows.com/bioworkflows/public_preview/ca7f9ec8a74e09f79d5d2c1771189892e2bd70592bd3457dadde86e34364ea4b.jpg)
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...
![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...
![mosaicatcher-pipeline](https://media.bioworkflows.com/bioworkflows/public_preview/c48c164807fd814e269fb9d2bd621165c0b5c3e492cd94db57e6d55999df4ed1.jpg)
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
![cd4-csaw](https://media.bioworkflows.com/bioworkflows/public_preview/c3fb43f19325460b909d855f597b7fb2d3baf7cd6a2cb5ab8a888cf85f959941.jpg)
Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set
This is the code for a re-analysis of a [GEO dataset][1] that I
originally analyzed for [this paper][2] using statistical met...
BSgenome.Hsapiens.UCSC.hg19
BSgenome.Hsapiens.UCSC.hg38
Gene ID
Peak calling
Quality control report
macs2
ucsc-liftover
BEDTools
BiocParallel
Bowtie 2
csaw
Cufflinks
GenomicAlignments
GenomicRanges
GLUE
graphite
GSEABase
HISAT2
kallisto
Quant
rtracklayer
Salmon
SAMtools
Snakemake
SRAdb
STAR
SummarizedExperiment
assertthat
dplyr
forcats
future
getopt
ggforce
ggplot2
here
ks
magrittr
optparse
reshape2
rex
rlang
scales
stringr
rpy2
rctutils
ChIP-seq
![strainsifter](https://media.bioworkflows.com/bioworkflows/public_preview/8f3bc15695a18b725d89f557a3abf8d8e15eb402002ac362d433e51465809ba7.jpg)
A straightforward bioinformatic pipeline for detecting a bacterial strain in one or more metagenome(s).
A straightforward bioinformatic pipeline for detecting the presence of a bacterial strain in one or more metagenome(s). Strai...