Genome-wide extraction of real-valued signals hidden in noisy multisample HTS data
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Sep 6, 2026 - Python
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cut-and-run
Here are 8 public repositories matching this topic...
Step-by-step instructions and Snakemake pipeline for processing Cut&Run data
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Sep 8, 2023 - Python
bowtie2 + MACS3 peak calling (Snakemake DAG, SLURM profile) on public CUT&Tag data -- honest CUT&RUN/CUT&Tag disclosure
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Jul 28, 2026 - Python
Which normalization method recovers a genome-wide change in CUT&RUN signal? A Nextflow benchmark scored against a dataset with known ground truth.
bioinformatics genomics nextflow reproducible-research chromatin normalization epigenomics spike-in cut-and-run differential-binding
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Sep 5, 2026 - Python
Personal portfolio of Dr. Mallikarjuna Thippana — computational biologist specializing in genomics & epigenomics (bulk RNA-seq, ChIP-seq, ATAC-seq, CUT&RUN), single-cell & spatial multi-omics, and statistical ML for biological data.
github-pages portfolio data-science bioinformatics rna-seq personal-website computational-biology cancer-genomics chip-seq atac-seq single-cell-genomics epigenomics spatial-transcriptomics cut-and-run phd-portfolio
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Jul 4, 2026 - HTML
Self-hosted CUT&RUN bioinformatics platform for the Ferguson Lab at UCSD. Replicates CUTANA Cloud and extends it with trimming, SEACR/MACS2, DiffBind, custom heatmaps, Pearson correlation, & Roman normalization. React + FastAPI + PostgreSQL on EC2.
react bioinformatics pipeline genomics postgresql igv chromatin epigenomics peak-calling fastapi diffbind cut-and-run
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Aug 26, 2026 - Python
qPCR Plate Planner is a browser-based tool to streamline the design, execution, and analysis of qPCR experiments. To have the AI functionality visit https://huggingface.co/spaces/mahmood-iab/qPCR-Plate-Planner-AI
epigenetics workflow-automation experimental-design qpcr-analysis gene-quantification master-mix plate-layout-design cut-and-run workflow-automation-tools fold-change-analysis chip-qpcr 384-well ddct-analysis chromatin-enrichment
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May 12, 2026 - HTML
A python-driven CUT&RUN pipeline analysis developed at the Phillips Lab (University of Pennsylvania) tailored to batch execution at a HPC environment.
bioinformatics bioinformatics-pipeline bioinformatics-analysis bioinformatics-scripts chipseq cut-and-run cut-and-tag
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Sep 9, 2026 - R
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