vanheeringen-lab

genomepy

genes and genomes at your fingertips

seq2science

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.

gimmemotifs

Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed installation instructions and usage examples.

ANANSE

Prediction of key transcription factors in cell fate determination using enhancer networks. See full ANANSE documentation for detailed installation instructions and usage examples.

scepia

Single Cell Epigenome-based Inference of Activity

psap

CLI interface for the PSAP classifier. PSAP implements a RandomForest approach to predict the probability of proteins to mediate protein phase separation (PPS)

Transcriptional_Burst_Kinetics

cfb_book

Textbook for the Computation for Biologists course @ Radboud University

anansnake

Automate long-running ANANSE analyses with snakemake

gimme-analysis

learnr.proto

aho_corasick

fast motif scanning, but exploding memory

ANANSE-CAGE

Supporting scripts and notebooks detailing how to use ANANSE with CAGE data.

ANANSE-manuscript

Notebook files describing analyses in the ANANSE paper (Xu et al. 2021)

cfb_temp

DevelopmentalRegulation_old

living analysis, https://vanheeringen-lab.github.io/DevelopmentalRegulation/

GBD_data

Datasets for the Genomics and Big Data course

genomepy_manuscript

GroupMeetings

learnr.dashboard

newproject

peaksql

Dynamic machine learning database for genomics.

pytxi

seq2science-FAQ

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.

seq2science-profiles