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@FrietzeLabUVM Frietze Lab @ UVM

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    18 repositories

    • chiptsne2

      Public
      General ChIPseq and epigenetic-seq workflow R package with support for t-SNE and UMAP to discover combinatorial epigenetic patterns.
      R
      •
      Other
      •1•0•0•0•Updated Apr 11, 2025Apr 11, 2025

    • ssvQC

      Public
      R package for QC of enrichment based NGS assays. ChIP-seq, cut&run, ATAC-seq, etc.
      bioinformaticsenrichmentchip-seqatac-seqpeaksngs-assaysr
      R
      •
      Other
      •1•5•5•0•Updated Jan 15, 2025Jan 15, 2025

    • TAP

      Public
      Pipeline to process RNAseq and ChIPseq data. Outputs include gene counts, transcripts per million, alternate splicing events, SNP calls, and bigwigs. Supports both Docker and Singularity for all dependencies.
      bioinformaticspipelinernaseqrdnafastq-fileschipseq
      Shell
      •
      Apache License 2.0
      •0•1•1•0•Updated Dec 3, 2024Dec 3, 2024

    • peaksat

      Public
      R package to do peak saturation analysis for ChIP-seq.
      R
      •2•1•1•0•Updated Sep 30, 2024Sep 30, 2024

    • TAPhelpR

      Public
      R package to help with TAP pipeline outputs
      R
      •0•0•0•0•Updated Sep 19, 2024Sep 19, 2024

    • chiptsne

      Public
      Apply tSNE for analysis of ChIPseq and related dataset
      R
      •
      MIT License
      •0•0•0•0•Updated Apr 21, 2023Apr 21, 2023

    • EIDA_core_resources

      Public
      Scripts and other computational resources for the EIDA core
      MIT License
      •0•0•0•0•Updated Jun 27, 2022Jun 27, 2022

    • BRD_PPIN

      Public
      R
      •
      MIT License
      •0•1•0•0•Updated Nov 29, 2021Nov 29, 2021

    • easyGO

      Public
      Make it easier to with GO terms in R.
      R
      •
      Other
      •0•0•0•0•Updated Nov 9, 2021Nov 9, 2021

    • ATACseq

      Public
      Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
      Shell
      •
      GNU General Public License v3.0
      •37•0•0•0•Updated Sep 14, 2021Sep 14, 2021

    • cutruntools

      Public
      Python
      •
      GNU General Public License v2.0
      •0•1•0•0•Updated Jun 9, 2021Jun 9, 2021

    • helpful_scripts

      Public
      helpful R scripts for various purposes
      R
      •0•0•0•0•Updated Mar 8, 2021Mar 8, 2021

    • hsv1_cis_interactions_pipeline

      Public
      from 4c fastq files generate cis interactions and circos plots
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Feb 27, 2021Feb 27, 2021

    • 4c_window_method

      Public
      Michael Mariani variation of peak calling method by Kim et al. Nature 2020
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Feb 15, 2021Feb 15, 2021

    • chip_qc_development

      Public
      code for chip qc
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jan 20, 2021Jan 20, 2021

    • vacc_slurm_example_rna_seq

      Public
      An example of a script for RNA-Seq alignment using the SLURM job scheduler on VACC
      Shell
      •
      MIT License
      •0•0•0•0•Updated Nov 23, 2020Nov 23, 2020

    • dropseq

      Public
      For Dropseq single-cell RNA-seq analysis
      Shell
      •1•0•0•0•Updated Oct 12, 2020Oct 12, 2020

    • 4c_primer

      Public
      R
      •2•0•0•0•Updated Sep 22, 2020Sep 22, 2020