Frietze Lab @ UVM

Frietze Lab @ UVM's repositories

ssvQC

R package for QC of enrichment based NGS assays. ChIP-seq, cut&run, ATAC-seq, etc.

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peaksat

R package to do peak saturation analysis for ChIP-seq.

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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.

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4c_primer

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ATACseq

Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)

Language:ShellGPL-3.0000

chiptsne

Apply tSNE for analysis of ChIPseq and related dataset

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chiptsne2

General ChIPseq and epigenetic-seq workflow R package with support for t-SNE and UMAP to discover combinatorial epigenetic patterns.

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dropseq

For Dropseq single-cell RNA-seq analysis

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easyGO

Make it easier to with GO terms in R.

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EIDA_core_resources

Scripts and other computational resources for the EIDA core

MIT000

hsv1_cis_interactions_pipeline

from 4c fastq files generate cis interactions and circos plots

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TAPhelpR

R package to help with TAP pipeline outputs

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vacc_slurm_example_rna_seq

An example of a script for RNA-Seq alignment using the SLURM job scheduler on VACC

Language:ShellMIT000

4c_window_method

Michael Mariani variation of peak calling method by Kim et al. Nature 2020

GPL-3.0000

chip_qc_development

code for chip qc