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analysis-flow

NextFlow pipeline for automated analysis of processed RNA-Seq and Nascent data

base_content

Base content summary for genomic regions

bda_py_demos

Bayesian Data Analysis demos for Python

bidirectional-flow

Nextflow pipeline for detecting bidirectional transcripts from nascent RNA sequencing data.

bigwig

R interface to query UCSC bigWig files

cookbook-2nd-code

Code of the IPython Cookbook, Second Edition, by Cyrille Rossant, Packt Publishing 2018 [read-only repository]

cpbs7711_2020

dreg

Detecting Regulatory Elements using GRO-seq and PRO-seq

examplethesis

An example LaTeX template for CU Anschutz

fantom_lps

Clustering of FANTOM5 CAGE data processed using TFEA

genome_wavelets

Wavelet transformations of sequencing (genomic) data.

github-for-developers-7

hmm_sequencer

A script to generate genomic sequences from a background distribution.

mumerge_explore

Comparing mumerge regions with sample regions.

networktutorials

Repository for presentations and network inference tutorials

pyscenic

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

rutendos.github.io

Personal website

scenicprotocol

A scalable SCENIC workflow for single-cell gene regulatory network analysis

tfea

Transcription Factor Enrichment Analysis

tfit

A tool for modeling and annotating RNA polymerase II behavior

workshop