Nascent Transcription Processing Pipeline

General analysis of HiC data, including compartment A/B, domains and loops.

Hidden RNA profiles of cells in the tumor microenvironment accurately revealed by malignant cell fraction-informed deconvolution

Analysis of Chromosome Conformation Capture data (Hi-C)

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing

circular RNA quantification tools

Estimate locus specific human LINE-1 expression.

Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023

Detecting sites of genomic enrichment

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

Universal RObust Peak Annotator

Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal

bart2 package

Toolkit for processing sequences in FASTA/Q formats

Simple and extensible administrative interface framework for Flask

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.

Yet another redundant workflow engine

The complete sequence of a human genome

《架构整洁之道》中文翻译

Unix, R and python tools for genomics and data science

Contains files for the deep learning in genomics primer.

Template for writing a PhD thesis in Markdown

Model zoo for genomics

PRObabilistic Simulations of ScRNA-seq Tree-like Topologies

Webserver for motif discovery with higher-order Bayesian Markov Models (BaMMs)

De-novo motif discovery and optimization

Bayesian Markov Model motif discovery - An expectation maximization algorithm for the de novo discovery of enriched motifs as modelled by higher-order Markov models.

Bayesian Markov Model motif discovery tool version 2 - An expectation maximization algorithm for the de novo discovery of enriched motifs as modelled by higher-order Markov models.

PEnG-motif is an open-source software package for searching statistically overrepresented motifs (position specific weight matrices, PWMs) in a set of DNA sequences.