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RBioMIR

miRNA-seq analysis package

To cite in publication

Zhang J, Hadj-Moussa H, Storey KB. 2016. Current progress of high-throughput microRNA differential expression analysis and random forest gene selection for model and non-model systems: an R implementation. J Integr Bioinform. 13: 306.

NOTE:

  • (For testing only) For novel miRNA discovery, be sure to copy training.smir and test.smir files to your working directory, and install pcregrep and parallel commands.
  • Small RNA RNAseq file processing program mirna_processing.sh only supports UNIX/UNIX-like systems.

Installation:

  • Install devtools

    install.packages("devtools")
    
  • Install bioconductor

    if (!requireNamespace("BiocManager"))
        install.packages("BiocManager")
        
    BiocManager::install()
    
  • Install stable release

    devtools::install_github("jzhangc/git_RBioMIR/RBioMIR", repos = BiocManager::repositories())    
    
  • Install development build

    devtools::install_github("jzhangc/git_RBioMIR/RBioMIR", repos = BiocManager::repositories(), ref = "beta")  
    

Update log

0.2.6 (Jan.17.2022)
  - Small typo fixes

0.2.5 (Dec.23.2021)
  - S4 class "mircount" added as an improved miRNA read class over the S3 class "mir_count"

0.2.4 (Dec.7.2021)
  - New items added to the "mir_count" object
    - working_gene_annot_var_name: for the object derived from mirProcess(), the value for this is always "mirna"
    - target_annotation_file_processed

  - mirDeepProcess() function added to process conserved miRNA count resutls from miRDeep2
  - The "mir_count" object updated with "genes_complete_annotation" data frame
    - The print function for "mir_count" updated accordingly
  - The "mir_count" object's "raw_read_count" now uses gene names as row names

0.2.3 (Jan.17.2019)
  - New bioconductor installation instructions added
  
  
0.2.2
  - "files_processed" added to "mir_count" object
  - A bug fixed for mirProcess function where the function will improperly check target.annot.file even if it's set at NULL


0.2.1
  - Adjustments made to "mir_count" objects
    - The object now outputs genes and counts separately
    - The object now outputs library size for the samples
    
  - Bug fixes


0.2.0
  - New functions
    - S3 print function for "mir_count"
      
  - Updates to exisiting functions:
    - mirProcess() re-written, with:
      - simplied code base
      - foreach implementation of parallel computing
      - compatibility for UNIX/UNIX-like/Windows systems
      - non-mandatory naming convention for input .txt read count files
      - ability to take annotation file
      - output in S3 object "mir_count"
          
  - A preview of UNIX Shell program mirna_processing added
  - Other updates
      - Information page updated

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miRNA-seq downstream analysis package

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