kuanhao-chao/rnaseqr

📊 An R package of RNA-seq workflow

👋 Hi, I'm Kuan-Hao Chao

🎓 I'm currently a third-year Ph.D. Candidate in Computer Science at the Center for Computational Biology, Johns Hopkins University, working with Steven Salzberg and Mihaela Pertea. My academic journey started in Electrical Engineering at National Taiwan University (NTU), shifting towards computer science in my final year at the College of Engineering & Computer Science at Australian National University (ANU) 🦘🐨

🧬 My research interest intersects "graphs" with genomics and transcriptomics:

• In genome assembly, De Bruijn graphs are widely used. For an example of its application, check out my Han1 assembly, the first gapless Southern Chinese Han genome.
• For pangenome indexing, I've contributed to making the Wheeler graph recognition problem computationally feasible through innovative heuristic methods combined with an SMT solver (Learn more).
• In genome annotation, I have utilized graph-based methods to stitch together fragmented DNA and protein alignments, thereby assembling them into more accurate annotations. (Learn more).
• My transcriptome assembly work focuses on modeling RNA-Seq data using directed acyclic splice graphs, with ongoing research into graph neural networks to decode the complexities of RNA splicing. (Learn more).

💻 As a staunch advocate for open-source software, I invite you to explore my NEWS page for the latest updates on my projects.

💬 Feel free to reach out to me for collaborations, discussions, or just to say hi! Coffee chat! ☕️

🔍 Discover more about my work on my personal website.

rnaseqr's Issues

Error in PostRNASeqEnvironmentSet(path.prefix, genome.name, sample.pattern) : RNASeqEnvironmentSet() post-check ERROR

RNASeqEnvironmentSet(RNASeqRParam = yeast, which.trigger = "OUTSIDE", INSIDE.path.prefix = NA, install.hisat2 = TRUE, install.stringtie = TRUE, install.gffcompare = TRUE, check.s4.print = TRUE)

Directory Copying

● Copying From :/home/kuan-hao/R/x86_64-pc-linux-gnu-library/3.5/RNASeqRData/extdata/input_files/Saccharomyces_cerevisiae_XV_Ensembl.gtf

 ●           To :/tmp/yeast_example/gene_data/ref_genes/Saccharomyces_cerevisiae_XV_Ensembl.gtf

ls -al /tmp/yeast_example/gene_data/ref_genes

lrwxrwxrwx 1 root root 120 Apr 9 15:27 Saccharomyces_cerevisiae_XV_Ensembl.gtf -> /home/kuan-hao/R/x86_64-pc-linux-gnu-library/3.5/RNASeqRData/extdata/input_files/Saccharomyces_cerevisiae_XV_Ensembl.gtf

In Directory Copying section, Copying From path not on my server !!
"/home/kuan-hao/" Should be on the author's computer !!