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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.
      bioinformaticsenrichmentr
      bioinformaticsenrichmentrchip-seqatac-seqpeaksngs-assays
      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 …
      bioinformaticspipelinernaseq
      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•2•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
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