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.
- (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.
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")
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