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megadudes-evaluation
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Snakemake workflow: megadudes-evaluation
public

public

This is the template for a new Snakemake workflow. Replace this text with a comprehensive description covering the purpose an...
JSON dudes Diamond Pandas Pyteomics Snakemake matplotlib requests seaborn Sequence analysis
Free
15
acrs
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Robust Optogenetic Inhibition with Red-light-sensitive Anion-conducting Channelrh
public

public

This repository hosts the bioinformatic analysis worklow used in Oppermann et al (2023) Robust Optogenetic Inhibition with ...
APE Bio3D Biopython castor ggtree Gotree MAFFT API (EBI) Snakemake treeio trimAl dplyr ggnewscale ggplot2 photobiology readxl tidyr
Free
14
snakemake_tutorial
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Snakemake tutorial workflow with SCIF
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public

This repository implements the SnakeMake tutorial workflow and uses the Scientific Filesystem (SCIF) to provide a reproducibl...
BCFtools BWA SAMtools Snakemake
Free
7
scrnaseq_cellqc
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Single-Cell RNAseq Data Quality Control Workflow using Scanpy
public

public

Take an anndata file, and perform basic QC with scanpy. Produces a filtered AnnData object.
Data Sequencing quality control Data index Galaxy SCANPY scRNA-Seq WorkflowHub RNA-Seq
Free
drc_cellbased_outlierdetection
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Dose-Response Curve Fitting Workflow for Cell-Based Assay Data with KNIME HCS Extension
public

public

This workflow can be used to fit dose-response curves from normalised cell-based assay data (%confluence) using the KNIME HCS...
Konstanz Information Miner (KNIME) WorkflowHub Data visualisation
Free
lung_adenocarcinoma_vs_squamous_time
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Bio 470 project 2022. Bulk RNA scripts
public

public

This workflow performs a differential expression analysis using STAR and DESeq2 . It performs a wide range of quality...
DESeq2 biomaRt EnhancedVolcano PCAtools AnnotationHub BiocParallel ComplexHeatmap Cutadapt DESeq2 fgsea GFFutils limma MultiQC Pandas SAMtools Snakemake STAR circlize cowplot ggnewscale ggplot2 ggrepel GSA janitor msigdbr readr scales shades tidyverse
Free
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