Frietze Lab @ UVM
Bioinformatics software, scripts, and analysis projects developed by the Frietze Lab
Pinned Repositories
BRD_PPIN
chiptsne
Apply tSNE for analysis of ChIPseq and related dataset
chiptsne2
General ChIPseq and epigenetic-seq workflow R package with support for t-SNE and UMAP to discover combinatorial epigenetic patterns.
cutruntools
easyGO
Make it easier to with GO terms in R.
hsv1_cis_interactions_pipeline
from 4c fastq files generate cis interactions and circos plots
peaksat
R package to do peak saturation analysis for ChIP-seq.
ssvQC
R package for QC of enrichment based NGS assays. ChIP-seq, cut&run, ATAC-seq, etc.
TAP
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.
TAPhelpR
R package to help with TAP pipeline outputs
Frietze Lab @ UVM's Repositories
FrietzeLabUVM/ssvQC
R package for QC of enrichment based NGS assays. ChIP-seq, cut&run, ATAC-seq, etc.
FrietzeLabUVM/BRD_PPIN
FrietzeLabUVM/cutruntools
FrietzeLabUVM/peaksat
R package to do peak saturation analysis for ChIP-seq.
FrietzeLabUVM/TAP
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.
FrietzeLabUVM/4c_primer
FrietzeLabUVM/ATACseq
Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
FrietzeLabUVM/chiptsne
Apply tSNE for analysis of ChIPseq and related dataset
FrietzeLabUVM/chiptsne2
General ChIPseq and epigenetic-seq workflow R package with support for t-SNE and UMAP to discover combinatorial epigenetic patterns.
FrietzeLabUVM/dropseq
For Dropseq single-cell RNA-seq analysis
FrietzeLabUVM/easyGO
Make it easier to with GO terms in R.
FrietzeLabUVM/EIDA_core_resources
Scripts and other computational resources for the EIDA core
FrietzeLabUVM/hsv1_cis_interactions_pipeline
from 4c fastq files generate cis interactions and circos plots
FrietzeLabUVM/TAPhelpR
R package to help with TAP pipeline outputs
FrietzeLabUVM/vacc_slurm_example_rna_seq
An example of a script for RNA-Seq alignment using the SLURM job scheduler on VACC
FrietzeLabUVM/4c_window_method
Michael Mariani variation of peak calling method by Kim et al. Nature 2020
FrietzeLabUVM/chip_qc_development
code for chip qc
FrietzeLabUVM/helpful_scripts
helpful R scripts for various purposes