linxingchen
I am an associated project scientist in the Banfield Lab of UC Berkeley, using genome-resolved metagenomics to study microorganisms and their infecting viruses
UC BerkeleyCalifornia
Pinned Repositories
cobra
A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.
CRISPR
crispr analyses
FASTA
basic scripts for fasta file
FriendsDontLetFriends
Friends don't let friends make certain types of data visualization - What are they and why are they bad.
General
any general scripts
noveltree
NovelTree is a highly parallelized and computationally efficient phylogenomic workflow that infers gene families, gene family trees, species trees, and gene family evolutionary history.
PlasmidHunter
This tool predicts plasmid sequences from genomic and metagenomic assemblies using machine learning.
pullseq
Utility program for extracting sequences from a fasta/fastq file
shrinksam
C++ program to shrink the SAM file after a read-mapping
sickle
Windowed Adaptive Trimming for fastq files using quality
linxingchen's Repositories
linxingchen/cobra
A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.
linxingchen/FriendsDontLetFriends
Friends don't let friends make certain types of data visualization - What are they and why are they bad.
linxingchen/noveltree
NovelTree is a highly parallelized and computationally efficient phylogenomic workflow that infers gene families, gene family trees, species trees, and gene family evolutionary history.
linxingchen/PlasmidHunter
This tool predicts plasmid sequences from genomic and metagenomic assemblies using machine learning.
linxingchen/pprodigal
Python3 wrapper for parallelized gene prediction using Prodigal
linxingchen/prodigal-gv
A fork of Prodigal meant to improve gene calling for giant viruses and viruses that use alternative genetic codes
linxingchen/astra
pyHMMer-based sequence search and retrieval tool.
linxingchen/bioconda-recipes
Conda recipes for the bioconda channel.
linxingchen/Carter-and-Olm-Cell-2023---db-info
README for Zenodo archive associated with publication Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes
linxingchen/chainsaw
Rapidly Search and Hunt through Windows Forensic Artefacts
linxingchen/Complete-Python-3-Bootcamp
Course Files for Complete Python 3 Bootcamp Course on Udemy
linxingchen/contig-extender
linxingchen/defense-finder
Systematic search of all known anti-phage systems.
linxingchen/DRAM
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
linxingchen/fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
linxingchen/foldseek
Foldseek enables fast and sensitive comparisons of large structure sets.
linxingchen/genomad
geNomad: Identification of mobile genetic elements
linxingchen/Jorg
MAG Circularization Method
linxingchen/MGnifyR
R package for searching, downloading and analysis of EBI MGnify metagenomics data
linxingchen/MMseqs2
MMseqs2: ultra fast and sensitive search and clustering suite
linxingchen/nanopore_script
A snakemake assembly pipeline for hybrid metagenome sequencing
linxingchen/PhaGCN2.0
linxingchen/PhaGCN_newICTV
Update model for ICTV2022
linxingchen/phamb
Downstream processing of VAMB binning for Viral Elucidation
linxingchen/PlasX
PlasX, a machine learning classifier for identifying plasmid sequences based on genetic architecture
linxingchen/RoseTTAFold-All-Atom
linxingchen/sphae
NEW!!! Phage annotations and predictions. A spae is a prediction or foretelling. We'll foretell you what your phage is doing!
linxingchen/umap
Uniform Manifold Approximation and Projection
linxingchen/ViWrap
A wrapper to identify, bin, classify, and predict host-viral relationship for viruses
linxingchen/vsearch
Versatile open-source tool for microbiome analysis