All Published Workflows

4 workflows that have been reviewed and published

cd4-csaw
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Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set
public

public

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
Free
114
deepg4toolscomparison
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DeepG4ToolsComparison: A snakemake pipeline to run and evaluate G4’s DNA prediction tools
public

public

The predictions for differents tissues and cancer with DeepG4 is available here The code to generate the precision/recall...
BSgenome.Hsapiens.UCSC.hg19 Biopython Biostrings plyranges Snakemake tidyverse
Free
28
atac-seq
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ATAC-seq Data Analysis Workflow
public

public

#Snakemake workflow: ATAC-seq This is using the standard Snakemake workflow template. Replace this text with a comprehensive ...
BSgenome.Hsapiens.UCSC.hg19 BSgenome.Mmusculus.UCSC.mm10 TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Mmusculus.UCSC.mm10.knownGene macs2 PCAtools ROTS Rsamtools ATACseqQC BEDTools ChIPpeakAnno DESeq2 FeatureCounts homer MotifDb MultiQC Picard Rsubread SAMtools Snakemake STAR dplyr ggplot2 mgsub Trim_Galore ATAC-seq
Free
37
mpra-gwas-builder
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MPRA GWAS Builder: snakemake workflow
public

public

Robin Meyers (@robinmeyers) If you simply want to use this workflow, download and extract the latest release . If ...
BSgenome.Hsapiens.NCBI.GRCh38 BSgenome.Hsapiens.UCSC.hg19 SNPlocs.Hsapiens.dbSNP144.GRCh37 TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Hsapiens.UCSC.hg38.knownGene ucsc-liftover Biostrings Greedy algorithm for Set Cover problem haploR LDlinkR plyranges rtracklayer Snakemake VariantAnnotation cowplot doMC ggplot2 magrittr tidyverse
Free
17