All Published Workflows
215 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...
![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
![pyflow-rnaseq](https://media.bioworkflows.com/bioworkflows/public_preview/88cb5e4487296b82d57088487a14e8b60d61a131ad56f2ddedff38fe8e601de6.jpg)
RNAseq pipeline based on snakemake
If you use this pipeline, please cite:
If inputs are fastq files:
The output folder will be suffixed by _fq
I...
![iris](https://media.bioworkflows.com/bioworkflows/public_preview/667ad79c043f1f3b52bcaf7201f7e9cdf0c2984c711aae189fb65dfd2c7caf51.jpg)
IRIS: Isoform peptides from RNA splicing for Immunotherapy target Screening
Dependencies
Installation
Usage
Usage - individual functions (for customized pipelines)
...
![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
![tapseq_manuscript](https://media.bioworkflows.com/bioworkflows/public_preview/aeeb1fce3233427d6d70986f34812d798674901dc3b6fc6d8acc7a80ee611223.jpg)
Analysis code for the TAP-seq manuscript.
This repository contains code to reproduce the results presented in the article. It builds upon a snakemake workflow that...
bigWig
ucsc-liftover
BiocParallel
Biopython
Biostrings
BSgenome
Consensus
GenomicAlignments
GenomicFeatures
GenomicRanges
HiTC
Pandas
Picard
rtracklayer
SAMtools
Snakemake
STAR
Trimmomatic
corrplot
eulerr
factoextra
GGally
ggplot2
ggpubr
ggrepel
gridExtra
here
kableExtra
Matrix
optparse
plotly
pROC
readxl
tidyverse
numpy
plotly
![singlecell-ige](https://media.bioworkflows.com/bioworkflows/public_preview/707a46de9ac216428914b6375601c6422bb22c12c6d04fd21397a1dfafce2d97.jpg)
Alignment and antibody assembly pipelines for Croote et al. (Science, 2018)
Alignment and assembly workflows associated with Croote et al. (2018). These workflows were developed to analyze single human...
![snakemake-rnaseq](https://media.bioworkflows.com/bioworkflows/public_preview/6962e61d2f5d570479afda27e2991fede31cfb7a30a314242276c46e2f0d6ba3.jpg)
![fuccisinglecellseqpipeline](https://media.bioworkflows.com/bioworkflows/public_preview/49002a508a02c65cd3d585faf81870a55f16b5623a36edb63cf3147be288da9d.jpg)
Cell cycle analysis of single-cell proteomic and transcriptomic data for the FUCCI cell model -- RNA-Seq analysis pipeline
This repository contains the snakemake pipeline for analyzing the RNA sequencing data for ~1k single cells. The results o...
![bollito](https://media.bioworkflows.com/bioworkflows/public_preview/4de8370d383b468d05424d2c505163dca2a071af3c8dc4e689830bcfab13f8d8.jpg)
A single-cell RNA-seq pipeline
Pipeline status
bollito is a
Snakemake pipeline that performs a comprehensive single-cell RNA-seq analysis, co...
GenomeInfoDbData
qusage
slingshot
BiocParallel
Bowtie 2
FastQC
GFFutils
GSEA
MultiQC
patcHwork
pheatmap
SCANPY
Seurat
SingleCellExperiment
Snakemake
STAR
cluster
clustree
data.table
devtools
dplyr
future
ggplot2
htmltools
Matrix
openxlsx
RColorBrewer
reticulate
rgl
rmarkdown
scales
stringr
viridis
SeuratDisk
SeuratWrappers