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abc-enhancer-gene-prediction

Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)

coursera_capstone

A capstone project for Coursera's Applied Data Science Capstone Course

cutandrun

Snakemake process for trimming and alignment of Cut&Run sequencing

graph-generator

Python utility for generating PCA plots and heatmaps from expression data

hic-fast

HiC processing pipeline for fast alignment

hiv_chimfinder

ipa_pathwayparser

A set of scripts useful for parsing and graphing the results of IPA (Ingenuity Pathway Analysis) exported text files.

isoseq_processing

Snakemake for processing Isoseq reads

ngs-data-charmer

This repository hosts an automated NGS data analysis (RNA-seq and ChIP-seq) pipeline created using Snakemake.

ngsplot

Quick mining and visualization of NGS data by integrating genomic databases

re_discovery

REDa code

repcounter

RepCounter provides a lightweight, modular program for estimating the relative abundance of repeat families and classes in a next-generation sequencing project.

repenrich2

RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.

rpkm_generator

A python script for generating RPKM files

rrho2

seastar

SEASTAR - Systematic Evaluation of Alternative transcription STArt site in RNA

snake-rna

Pipeline for summarizing expression data for batches of public RNA-seq datasets

tama

Transcriptome Annotation by Modular Algorithms (for Iso-Seq data)

transcript_integrity

Code for generating the Transcript Integrity Index