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4c_primer

4c_window_method

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

atacseq

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

brd_ppin

chip_qc_development

code for chip qc

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

dropseq

For Dropseq single-cell RNA-seq analysis

easygo

Make it easier to with GO terms in R.

eida_core_resources

Scripts and other computational resources for the EIDA core

helpful_scripts

helpful R scripts for various purposes

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

vacc_slurm_example_rna_seq

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