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?
| # | Project | Description |
|---|---|---|
| [1] | eGPS_v2 | Source code of eGPS v2 - an advanced bioinformatics analysis platform, focus on the pathway evolutionary browser |
| [2] | egps-base | The core infrastructure of the eGPS v2 project. See the docs subdirectory for complete class documentation. |
| [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 |
| # | Project | Description |
|---|---|---|
| [5] | egps-heatmap | The heatmap module of eGPS v2 software platform |
| [6] | egps-chorddiagram | The chord diagram module of eGPS v2 software platform |
| [7] | egps-mutationPre | The genomic mutation presenter module of eGPS v2 software platform |
| [8] | egps-sanky-venn | The sanky plot module of eGPS v2 software platform |
| # | Project | Description |
|---|---|---|
| [9] | egps-genome.browser | The genome browser clone from IGV and modified for eGPS. |
| # | Project | Description |
|---|---|---|
| [10] | egps-SeqTools | The sequences tools for biologists(SeqTools), which are modules of eGPS v2 software platform |
| [11] | egps-pathway.evol.browser | 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 the eGPS v2 project. |
| [12] | egps-oneBuilder | GUI and CLI workflow for phylogenetic tree construction, tanglegram comparison, and optional Foldseek protein-structure similarity. |
| [13] | egps-million_evoltree | This tree builder is optimized for constructing phylogenetic trees from millions of OTUs using multi-threading acceleration. It is based on a modified version of the Neighbor-Joining Tree Algorithm, enhancing efficiency and processing speed while maintaining accuracy, making it ideal for large-scale genomic data. |
| # | Project | Description |
|---|---|---|
| [14] | Py4eGPS | The Python version library to adapt the power of the eGPS bioinformatic platform |
| [15] | R4eGPS | The R packege of the eGPS v2 |
| # | Project | Description |
|---|---|---|
| [16] | resolveS | A super-fast, memory-efficient tool for RNA-Seq strand specificity |
| [17] | ty | Personal R utils functions |
| [18] | pubmed_spider | Spider program for downloading article text from PubMed and PMC |
| [19] | ete | Python package for building and visualising trees (fork) |
| [20] | PathwayI | - |
⭐️ Stars and contributions are welcome!