Pinned Repositories
arxiv-downloader
A command line interface to download PDF files from https://arxiv.org.
CHM13
Ultra-long reads for CHM13 genome assembly
funannotate
Eukaryotic Genome Annotation Pipeline
iMGMC
Repository of the integrated mouse gut metagenomic catalog
jgi_meta_wdl
phanta
Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes
physpetools
PhySpeTree: automatically reconstructing phylogenetic tree
STRling
Detect novel (and reference) STR expansions from short-read data
pythseq's Repositories
pythseq/arxiv-downloader
A command line interface to download PDF files from https://arxiv.org.
pythseq/phanta
Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes
pythseq/bash-handbook
:book: For those who wanna learn Bash
pythseq/bioframe
Genomic Interval Operations on Pandas DataFrames
pythseq/Book-Mathematical-Foundation-of-Reinforcement-Learning
This is the homepage of a new book entitled "Mathematical Foundations of Reinforcement Learning."
pythseq/books-collection
To the programmer's open source and free books collection 给程序员的开源、免费书籍收集，图书集合。
pythseq/cactus
Official home of genome aligner based upon notion of Cactus graphs
pythseq/colora
A snakemake workflow for de novo genome assembly. It produces chromosome-scale primary/phased assemblies complete with organelles (mitochondrion and/or chloroplast). It automatically assesses the quality of the results.
pythseq/depth_vs_polishing_analysis
Repository to hold code and data for the How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies manuscript
pythseq/docker_practice
Learn and understand Docker&Container technologies, with real DevOps practice!
pythseq/enrichment-analysis-training
Course material for Enrichment analysis course by SIB
pythseq/GENESPACE
pythseq/geocompr
Geocomputation with R: an open source book
pythseq/gpt4all
gpt4all: run open-source LLMs anywhere
pythseq/herro
HERRO is a highly-accurate, haplotype-aware, deep-learning tool for error correction of Nanopore R10.4.1 or R9.4.1 reads (read length of >= 10 kbps is recommended).
pythseq/inkscaping-graphs
TheBGAcademy 2024: Making graphs with Inkscape
pythseq/labview_book
LabVIEW Tutorials
pythseq/MetaCerberus
Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focus of shotgun metaomics data
pythseq/MicroFinder
order a FASTA file by microchromosome specific genes
pythseq/ngless
NGLess: NGS with less work
pythseq/phables
🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes
pythseq/progit2
Pro Git 2nd Edition
pythseq/puter
🌐 The Internet OS! Free, Open-Source, and Self-Hostable!
pythseq/python-guide
Python best practices guidebook, written for humans.
pythseq/python_devops_book
[Book-2020] Python For DevOps: Learn Ruthlessly Effective Automation
pythseq/RAT_paper
pythseq/state-of-open-source-ai
:closed_book: Clarity in the current fast-paced mess of Open Source innovation
pythseq/theMLbook
The Python code to reproduce the illustrations from The Hundred-Page Machine Learning Book.
pythseq/tidy-text-mining
Manuscript of the book "Tidy Text Mining with R" by Julia Silge and David Robinson
pythseq/training_marbl_verkko
Genome Assembly 102