AlphaFold 3 inference pipeline.

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.

Human and mouse genome assemblies customized for rDNA mapping

Data of genome annotation from full-stack ChromHMM model trained with 1032 datasets from 127 reference epigenomes

A peak-calling tool package for functional genomic and other data sets.

Notes on ChIP-seq and other-seq-related tools

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

Basic operations on the space of numerical functions defined on the genome using lazy evaluators for flexibility and efficiency

IDR

A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.

A simple RNA-Seq differential gene expression pipeline using Nextflow

Applying IDR analysis to Homer peaks.

python (cython) wrapper for https://github.com/ryanlayer/giggle for fast interval searching of huge datasets.

Interval data structure

Github Pages template based upon HTML and Markdown for personal, portfolio-based websites.

MUltiScale enrIchment Calling for ChIP-Seq Datasets

Tool for plotting sequencing data along genomic coordinates.

Irreproducibility Discovery Rate analysis script

An introduction to various methods/approaches for the analysis of peaks generated from ChIP-seq / CUT&RUN / ATAC-seq

DNA methylation studies of mammalian species

[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome

GENA-LM is a transformer masked language model trained on human DNA sequence.

Easily install and load packages from the tidyomcis ecosystem

Read-based phasing of genomic variants, also called haplotype assembly

Nextflow workflow for automatic repeat detection, classification and masking

Predicted G4 Sequences in the Human Genome by G4Hunter Software

Collection of G-quadruplex prediction tools