All Published Workflows

4 workflows that have been reviewed and published

multicondition-deseq2-enrichment
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Workflow dervied form https://github.com/snakemake-workflows/rna-seq-star-deseq2 for multi condition Deseq2 and enrichment analyis
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public

Snakemake workflow for running differential expression and enrichment analyses for experimental setups with multiple groups o...
org.Mm.eg.db CSV Data Enrichment analysis GO-term enrichment data biomaRt EnhancedVolcano OmnipathR PCAtools AnnotationHub BiocParallel CARNIVAL clusterProfiler ComplexHeatmap Consensus decoupleR DESeq2 enrichplot ensembldb FeatureCounts GFFutils GLUE GSEA GSEABase mitch MultiQC Pandas patcHwork pheatmap PIANO progeny Snakemake UpSetR viper broom cowplot dplyr ggplot2 ggraph ggupset knitr magrittr msigdbr network openxlsx plyr purrr RColorBrewer readr reshape2 scales snowfall svglite tibble tidygraph tidyr tidyverse visNetwork Gene expression
Free
121
genesetenrichment
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Snakemake pipeline for Gene Set Enrichment: pathway and GO enrichment analysis
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public

Author: Sherine Awad Change the config.yaml file appropriately according to your data. Update parameters of Genrich in the co...
org.Hs.eg.db org.Mm.eg.db biomaRt AnnotationDbi edgeR gage pathview Snakemake data.table dplyr gplots magrittr
Free
4
gr-mediated_gene_repression
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Code for the manuscript "Machine learning reveals STAT motifs as predictors for GR-mediated gene repression"
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public

TODO: Add citation once paper is accepted Software dependencies
BSgenome.Mmusculus.UCSC.mm10 BSgenome.Mmusculus.UCSC.mm9 org.Mm.eg.db TxDb.Mmusculus.UCSC.mm10.knownGene macs2 biomaRt universalmotif BEDTools Bowtie 2 CAGEr ChIPpeakAnno ChIPseeker ComplexHeatmap Consensus Cutadapt DeepTools DESeq2 FastQC FiMO genomation GenomicRanges MEME memes MultiQC Picard plyranges rtracklayer SAMtools Snakemake topGO circlize data.table dplyr ggplot2 ggpubr glmnet here optparse plsgenomics plyr png RColorBrewer stringr
Free
97
rnaseq-workflow
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Differential Gene Expression using RNA-Seq
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public

RNAseq is becoming the one of the most prominent methods for measuring celluar responses. Not only does RNAseq have the abili...
GO.db org.Hs.eg.db org.Mm.eg.db Differential gene expression profiling biomaRt PCAtools clusterProfiler DESeq2 DOSE FastQC FeatureCounts gage genefilter MultiQC pathview pheatmap ReactomePA SortMeRNA STAR topGO dplyr ggplot2 ggsci knitr RColorBrewer Trim_Galore RNA-Seq
Free
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