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RNASeqR

An R package of RNA-seq workflow


IEEE/ACM Transactions on Computational Biology and Bioinformatics (preprint): [link]

IEEE Xplore Digital Library: [PDF]

K. Chao et al., "RNASeqR: an R package for automated two-group RNA-Seq analysis workflow," in IEEE/ACM Transactions on Computational Biology and Bioinformatics. doi: 10.1109/TCBB.2019.2956708


Bioconductor Links:

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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 !!

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