Jake Lehle, Ph.D.'s Projects
ENCODE ATAC-seq pipeline
List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.
BCR evaluator is used to evaluate bisulfite conversion ratio in WGSBS experiment
Conda recipes for the bioconda channel.
Code for Mastering Python for Bioinformatics (O'Reilly, 2021, ISBN 9781098100889)
This repository contains scripts that can used to processing sequencing data and solutions to other bioinformatic problems.
Bioinformatics one liners from Ming Tang
BISulfite-seq CUI Toolkit
DNA methylation and variant Caller for Bisulfite Sequencing Data.
This is a pipeline I used while at UTSA to determine DEG from bulk RNA-seq experiment data. This is intended as a teaching tool for anyone learning to code and use the super computing cluster at UTSA regularly and contains in-depth step-by-step instructions to get started pulling and analyzing bulk RNA-seq datasets.
bumphunter
fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
A BioWDL pipeline for processing ChIP-seq data.
ENCODE ChIP-seq pipeline
:dart: ChIP peak Annotation, Comparison and Visualization
This is a repo that I use to set up snakemake cli quickly
command line interface (CLI) using click
This Snakemake pipeline implements the GATK best-practices workflow
ERVmap is one part curated database of human proviral ERV loci and one part a stringent algorithm to determine which ERVs are transcribed in their RNA seq data.
Paired End and Single End Fastq Coverage Downsampling
GEM-Mapper v3
gemBS is a bioinformatics pipeline designed for high throughput analysis of DNA methylation from Whole Genome Bisulfite Sequencing data (WGBS).
Blendshape and kinematics calculator for Mediapipe/Tensorflow.js Face, Eyes, Pose, and Finger tracking models.
Bostongene cell deconvolution algorithm from RNAseq
UCSC Genome Browser source tree. Stable branch: "beta".
Markdown Cheatsheet for Github Readme.md
✨ Build AI interfaces that spark joy
MR. PARETO - Modules & Recipes for Pragmatic Augmentation of Research Efficiency Towards Optimum