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yudalang3/README.md

Dalang Yu 👋

I focus on converting biological problems into computational formulations, with research spanning evolutionary biology, cell signaling, and software dev.

期待生物学的ChatGPT时刻，也许是通用AI虚拟细胞？
Looking forward to the ChatGPT moment in biology, perhaps a general AI virtual cell?

🧬 eGPS Suite

Core Framework

# Project Description
[1] eGPS_v2.1 The distribution entry point for eGPS software, combining all built-in and plug-in modules for download
[2] egps-base The core infrastructure of the eGPS2 project
[3] egps-shell The GUI mainframe extends by the eGPS-base
[4] egps-module-dev-evo A role model for software development of the eGPS module

Visualization Modules

# Project Description
[5] egps-heatmap The heatmap module of eGPS 2.1 software platform
[6] egps-chorddiagram The chord diagram module of eGPS 2.1 software platform
[7] egps-mutationPre The genomic mutation presenter module of eGPS 2.1
[8] egps-sanky-venn The sanky plot module of eGPS 2.1 software platform

Analysis Tools

# Project Description
[9] egps-SeqTools The sequences tools for biologists (SeqTools), modules of eGPS 2.1
[10] egps-pathway.evol.browser Biological pathway evolution across the animal phylum
[11] egps-oneBuilder Linux phylogenetic workflow for protein and DNA/CDS
[12] egps-million_evoltree Tree builder optimized for millions of OTUs using multi-threading

Language Bindings

# Project Description
[13] Py4eGPS The Python version library to adapt the power of the eGPS bioinformatic platform
[14] R4eGPS The R package of the eGPS 2.0

🔧 Standalone Tools

# Project Description
[15] resolveS A super-fast, memory-efficient tool for RNA-Seq strand specificity
[16] ty Personal R utils functions
[17] pubmed_spider Spider program for downloading article text from PubMed and PMC
[18] ete Python package for building and visualising trees (fork)
[19] PathwayI -

📫 Contact

⭐️ Stars and contributions are welcome!

Pinned Loading

  1. resolveS resolveS Public

    A super-fast, memory-efficient tool for automatically determining RNA-Seq strand specificity. Designed for seamless integration into QC pipelines, it ensures accurate parameter configuration for do…

    Shell 8

  2. egps-base egps-base Public

    The core infrastructure of the eGPS2 project. See the `docs` subdirectory for complete class documentation.

    Java 5 1

  3. egps-shell egps-shell Public

    The GUI mainframe extends by the eGPS-base

    Java 5 1

  4. egps-pathway.evol.browser egps-pathway.evol.browser Public

    Biological pathway evolution across the animal phylum, a comprehensive complex GUI module with full support of the interactive GUI operations and rich functionilities. This is a concrete module for…

    Java 4

  5. eGPS_v2.1 eGPS_v2.1 Public

    Source code of eGPS 2.1 - an advanced bioinformatics analysis platform

    5

  6. egps-oneBuilder egps-oneBuilder Public

    Linux phylogenetic workflow for protein and DNA/CDS with CLI batch runs, Java GUI interactive parameter tuning, tree inference, summary heatmaps, and tanglegram comparison.

    Java