Pinned Repositories
2bRAD-M
args_oap
ARGs-OAP: Online Analysis Pipeline for Antibiotic Resistance Genes Detection from Metagenomic Data Using an Integrated Structured ARG Database
fastcluster
Fast hierarchical clustering routines for R and Python.
gtdb2ncbi
GTDB => NCBI
bioconda-recipes
Conda recipes for the bioconda channel.
atlas
ATLAS - Three commands to start analyzing your metagenome data
metapi
A general metagenomics data mining system focus on robust microbiome research
quantpi
Microbiome profiling
rnapi
RNA seq analysis pipeline
snakemake-wrappers
This is the development home of the Snakemake wrapper repository, see
alienzj's Repositories
alienzj/gtdb.ecogenomic.org
https://gtdb.ecogenomic.org/
alienzj/alienzj.github.io
ZJ Org Blog
alienzj/alignment-and-variant-calling-tutorial
basic walk-throughs for alignment and variant calling from NGS sequencing data
alienzj/arcasHLA
Fast and accurate in silico inference of HLA genotypes from RNA-seq
alienzj/atlas
ATLAS - Three commands to start analysing your metagenome data
alienzj/biotk
Daily work debugging and biotk development with Mistral-7B
alienzj/dirscan
A high performance tool for summarizing large directories or drives
alienzj/doom.d
doom-emacs private configuration
alienzj/dotfiles
And I say hey, what's going on?
alienzj/figaro
An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters
alienzj/floria
Strain-level haplotyping for metagenomes with short or long-reads.
alienzj/ggml
Tensor library for machine learning
alienzj/iskylims
is an open-source LIMS (laboratory Information Management System) for Next Generation Sequencing sample management, statistics and reports, and bioinformatics analysis service management.
alienzj/lefse
alienzj/llama.cpp
LLM inference in C/C++
alienzj/llama2.c
Inference Llama 2 in one file of pure C
alienzj/llm.c
LLM training in simple, raw C/CUDA
alienzj/magick.css
magically playful, yet simple styling. all in one file.
alienzj/medi
Metagenomic Estimation of Dietary Intake and Content.
alienzj/MetaPhlAn
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
alienzj/MicrobiotaProcess
alienzj/ollama-ui
Simple HTML UI for Ollama
alienzj/phanta
Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes
alienzj/radEmu
alienzj/SemiBin
alienzj/slurmzy
Slurm wrapper scripts
alienzj/ugene
UGENE is free open-source cross-platform bioinformatics software
alienzj/vamb
Variational autoencoder for metagenomic binning
alienzj/whisper.cpp
Port of OpenAI's Whisper model in C/C++
alienzj/Write_A_Genome_Assembler_With_IPython
The repository keeps the files for an IPython notebook on about how to make a simple genome assembler using python