xzhuo

xzhuo's Stars

• microsoft/JARVIS

  JARVIS, a system to connect LLMs with ML community. Paper: https://arxiv.org/pdf/2303.17580.pdf

  Language:Python23.6k3821782k

• rust-bio/rust-bio

  This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.

  Language:Rust1.6k71196204

• mundimark/awesome-markdown-editors

  A collection of awesome markdown editors & (pre)viewers for Linux, Apple OS X, Microsoft Windows, the World Wide Web & more

  1.1k297119

• vgteam/vg

  tools for working with genome variation graphs

  Language:C++1.1k482.1k194

• cmdcolin/awesome-genome-visualization

  A list of interesting genome browser or genome-browser-like implementations

  Language:TypeScript836289108

• tanghaibao/jcvi

  Python library to facilitate genome assembly, annotation, and comparative genomics

  Language:Python74236477187

• nanoporetech/dorado

  Oxford Nanopore's Basecaller

  Language:C++493321k59

• zaeleus/noodles

  Bioinformatics I/O libraries in Rust

  Language:Rust4852221952

• nanoporetech/bonito

  A PyTorch Basecaller for Oxford Nanopore Reads

  Language:Python38935338120

• bioconvert/bioconvert

  Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

  Language:Python3652027444

• pangenome/pggb

  the pangenome graph builder

  Language:Shell3611316639

• oushujun/EDTA

  Extensive de-novo TE Annotator

  Language:Perl336949173

• pangenome/odgi

  Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs

  Language:C++1921414539

• dpryan79/MethylDackel

  A (mostly) universal methylation extractor for BS-seq experiments.

  Language:C160711242

• adamewing/methylartist

  Tools for plotting methylation data in various ways

  Language:Python12859110

• marbl/ModDotPlot

  Language:Python11211208

• cgroza/GraffiTE

  GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.

  Language:R1074344

• informationsea/transanno

  accurate LiftOver tool for new genome assemblies

  Language:Rust1065911

• KolmogorovLab/Severus

  A tool for somatic structural variant calling using long reads

  Language:Python1025244

• mrvollger/rustybam

  bioinformatics toolkit in rust

  Language:Rust783142

• PacificBiosciences/pb-CpG-tools

  Collection of tools for the analysis of CpG data

  707596

• PengNi/ccsmeth

  Detecting DNA methylation from PacBio CCS reads

  Language:Python7015110

• lh3/jstreeview

  Interactive phylogenetic tree viewer/editor

  Language:JavaScript46203

• nclark-lab/RERconverge

  Analysis of convergence between organismal traits and DNA/protein sequences

  Language:HTML44106826

• dohlee/metheor

  :comet: Ultrafast DNA methylation heterogeneity calculation from bisulfite alignments (Lee et al., PLOS Computational Biology. 2023)

  Language:Rust433188

• fiberseq/fibertools-rs

  Tools for fiberseq data written in rust.

  Language:Rust422345

• adamewing/tldr

  Identify and annotate TE-mediated insertions in long-read sequence data

  Language:Python403414

• hyungjoo-lee/wgbs

  WGBS processing pipeline

  Language:Shell2

• ChangxuFan/wgbs

  snake file of wgbs pipeline

  1

• debugpoint136/comparative-selection-widget

  Tree widget for selection of species for http://comparativegateway.wustl.edu

  Language:CSS1300