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atac-seq-pipeline

ENCODE ATAC-seq pipeline

awesome-single-cell

List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.

bcr_evaluator

BCR evaluator is used to evaluate bisulfite conversion ratio in WGSBS experiment

bioconda-recipes

Conda recipes for the bioconda channel.

biofx_python

Code for Mastering Python for Bioinformatics (O'Reilly, 2021, ISBN 9781098100889)

bioinformatic-toolbox

This repository contains scripts that can used to processing sequencing data and solutions to other bioinformatic problems.

bioinformatics-one-liners

Bioinformatics one liners from Ming Tang

biscuit

BISulfite-seq CUI Toolkit

bs_call

DNA methylation and variant Caller for Bisulfite Sequencing Data.

bulk_rna-seq

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

bumphunter

bwa-meth

fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome

chip-seq

A BioWDL pipeline for processing ChIP-seq data.

chip-seq-pipeline2

ENCODE ChIP-seq pipeline

chipseeker

:dart: ChIP peak Annotation, Comparison and Visualization

click

command line interface (CLI) using click

dna-seq-gatk-variant-calling

This Snakemake pipeline implements the GATK best-practices workflow

ervmap

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.

fastqcoverage

Paired End and Single End Fastq Coverage Downsampling

gem3-mapper

GEM-Mapper v3

gembs

gemBS is a bioinformatics pipeline designed for high throughput analysis of DNA methylation from Whole Genome Bisulfite Sequencing data (WGBS).

jakelehle

kalidokit

Blendshape and kinematics calculator for Mediapipe/Tensorflow.js Face, Eyes, Pose, and Finger tracking models.

kent

UCSC Genome Browser source tree. Stable branch: "beta".

markdown-cheatsheet

Markdown Cheatsheet for Github Readme.md

marvin

✨ Build AI interfaces that spark joy

mr.pareto

MR. PARETO - Modules & Recipes for Pragmatic Augmentation of Research Efficiency Towards Optimum

mspipe

new.py

Python program to write new Python programs

ngless

NGLess: NGS with less work