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phage-evo-paper
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Repository to store the analysis of the paper on phage evolution.
public

public

A Snakemake workflow for Phage directed evolution analysis .
Data index Analysis Report FastANI MMseqs NanoPlot SAMtools seqkit Snakemake Molecular evolution
Free
12
duxbl_cutandrun22
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Cut&Run pipeline used in Vega-Sendino, Olbrich et al.
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public

A workflow to process Cut&Run data on the NIH biowulf cluster . Most steps and some borrowed code from this paper , a...
macs2 preseq PCAtools Bowtie 2 DeepTools fastp FastQC MultiQC SAMtools Snakemake SPP caTools
Free
18
4c-workflow
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Generalized Snakemake workflow for R.4Cker
public

public

4C-Workflow is a snakemake implementation for the 4C-ker library. This generalized workflow aims to automate the 4C da...
BEDTools Bowtie 2 DESeq2 SAMtools Snakemake argparse yaml
Free
6
genetf
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Snakemake pipeline for scATAC metacell utilities such as primed and lineage specific scores, chromVAR, in-silico ChIP
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public

This repository contains a snakemake pipeline for utilities with ATAC and RNA metacells inferred using SEACells algor...
FiMO Pandas SCANPY Snakemake renv numpy scipy SEACells tqdm
Free
22
chipseq
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ChIP-seq peak-calling, QC and differential analysis pipeline (Snakemake port of the nextflow pipeline at https://nf-co.re/chipseq).
public

public

This is the template for a new Snakemake workflow. Replace this text with a comprehensive description covering the purpose an...
Data Peak calling Quality control report bedGraphToBigWig BEDTools BiocParallel BWA Cutadapt DESeq2 FastQC FeatureCounts GFFutils homer MaCS MultiQC Pandas pheatmap Picard SAMtools Snakemake UpSetR vsn ggplot2 lattice optparse RColorBrewer reshape2 scales tidyverse pysam PyYAML smart-open ChIP-seq
Free
117
simple-snakemake-secondary-workflow
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Demo Snakemake workflow - small and runs quickly for testing purposes.
public

public

Small demo workflow following best practice template for Snakemake workflows . Just includes bowtie2, fastqc and trim_gal...
raw sequence reads Expression analysis Report Bowtie 2 FastQC SAMtools Snakemake Trim_Galore Genomics
Free
5

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