vanheeringen-lab

ANANSE

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

cfb_book

Textbook for the Computation for Biologists course @ Radboud University

genomepy

genes and genomes at your fingertips

gimme-analysis

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.

learnr.proto

psap

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

scepia

Single Cell Epigenome-based Inference of Activity

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.

Transcriptional_Burst_Kinetics

vanheeringen-lab/genomepy

genes and genomes at your fingertips

vanheeringen-lab/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.

vanheeringen-lab/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.

vanheeringen-lab/ANANSE

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

vanheeringen-lab/scepia

Single Cell Epigenome-based Inference of Activity

vanheeringen-lab/psap

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

vanheeringen-lab/Transcriptional_Burst_Kinetics

vanheeringen-lab/cfb_book

Textbook for the Computation for Biologists course @ Radboud University

vanheeringen-lab/anansnake

Automate long-running ANANSE analyses with snakemake

vanheeringen-lab/gimme-analysis

vanheeringen-lab/learnr.proto

vanheeringen-lab/ANANSE-CAGE

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

vanheeringen-lab/GroupMeetings

vanheeringen-lab/aho_corasick

fast motif scanning, but exploding memory

vanheeringen-lab/ANANSE-manuscript

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

vanheeringen-lab/cfb_temp

vanheeringen-lab/DevelopmentalRegulation_old

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

vanheeringen-lab/GBD_data

Datasets for the Genomics and Big Data course

vanheeringen-lab/genomepy_manuscript

vanheeringen-lab/learnr.dashboard

vanheeringen-lab/newproject

vanheeringen-lab/peaksql

Dynamic machine learning database for genomics.

vanheeringen-lab/phylotypic_hourglass

vanheeringen-lab/pytxi

vanheeringen-lab/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.

vanheeringen-lab/seq2science-profiles