zhanxiangzong

zhanxiangzong's Stars

• ollama/ollama

  Get up and running with Llama 3.2, Mistral, Gemma 2, and other large language models.

  Language:Go92k5444.5k7.2k

• nomic-ai/gpt4all

  GPT4All: Run Local LLMs on Any Device. Open-source and available for commercial use.

  Language:C++69.7k6391.9k7.6k

• danielecook/Awesome-Bioinformatics

  A curated list of awesome Bioinformatics libraries and software.

  3.1k17010608

• kblin/ncbi-genome-download

  Scripts to download genomes from the NCBI FTP servers

  Language:Python93935144175

• nf-core/rnaseq

  RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

  Language:Nextflow878150644699

• OmicsML/awesome-deep-learning-single-cell-papers

  67231587

• kcleal/gw

  Genome browser and variant annotation

  Language:C++2706197

• Boyle-Lab/Blacklist

  Application for making ENCODE Blacklists

  Language:C++26484036

• lgmgeo/AnnotSV

  Annotation and Ranking of Structural Variation

  Language:Tcl2141125235

• Genentech/gReLU

  gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.

  Language:Python206112020

• gpertea/gffcompare

  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF

  Language:C++199149032

• Marsilea-viz/marsilea

  Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)

  Language:Python1632386

• moiexpositoalonsolab/grenepipe

  A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles.

  Language:Python8745521

• xihaoli/STAARpipeline

  An R package for performing association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using STAARpipeline

  Language:R5982018

• hahnlab/CAGEE

  Computational Analysis of Gene Expression Evolution

  Language:C++357232

• minmarg/gtalign_alpha

  GTalign, HPC protein structure alignment, superposition and search (alpha release)

  Language:Cuda33312

• PacktPublishing/Deep-Learning-for-Genomics-

  Language:Jupyter Notebook286114

• liu3zhenlab/homotools

  Language:HTML19403

• mcvickerlab/GenVarLoader

  Pipeline for efficient genomic data processing.

  Language:Python16172

• SNU-CSSB/RF2-Lite

  Language:Python13104

• kundajelab/DART-Eval

  Language:Jupyter Notebook10400

• DavideBrex/SpikeFlow

  Pipeline to analyse ChIP-Rx data, i.e ChIP-Seq with reference exogenous genome spike-in normalization

  Language:Python8100

• openlifescience-ai/Awesome-Genomic-LLMs

  A curated list of awesome resources, papers, datasets, and tools related to Genomic LLMs. This repository aims to provide a comprehensive collection of materials to facilitate research, learning, and development in the field of Genomic LLMs.

  8102

• ychuest/Awesome-LLMs-meet-genomes

  Explore a comprehensive collection of basic theories, applications, papers, and best practices about Large Language Models (LLMs) in genomes.

  8

• ajw2329/junctionCounts

  Utils for identifying pairwise alternative splicing events and quantifying them using junction reads.

  Language:Python61110

• FuhaiLiAiLab/mosGraphFlow

  Multi-Scale Multi-Hop Flow for Interpreting Mechanism of Signaling

  Language:Jupyter Notebook62

• uclahs-cds/metapipeline-DNA

  Nextflow pipeline to convert BAM to FASTQ, align, perform QC, assess targeted coverage, call gSNP, call sSNV, call mtSNV, call SVs, call sCNA, and perform subclonal reconstruction

  Language:Nextflow44920

• alekseyzimin/WheresWalker

  Language:Perl3300

• EUCANCan/variant-callers

  Scripts and containers to run the variant callers originally used in ONCOLINER

  Language:Shell2300

• karakulahg/regulaTER

  Language:R10