| Title: | SummarizedExperiment for the microRNAome project |
|---|---|
| Description: | This package provides a SummarizedExperiment object of read counts for microRNAs across tissues, cell-types, and cancer cell-lines. The read count matrix was prepared and provided by the author of the study: Towards the human cellular microRNAome. |
| Authors: | Matthew N. McCall <[email protected]>, Marc K. Halushka <[email protected]>, Arun H. Patil <[email protected]> |
| Maintainer: | Matthew N. McCall <[email protected]> |
| License: | GPL (>= 2) |
| Version: | 1.34.0 |
| Built: | 2026-10-10 11:10:38 UTC |
| Source: | https://github.com/bioc/microRNAome |
Read counts per miRNA for the microRNAome collection of RNA-Seq experiments
data("microRNAome")data("microRNAome")
SummarizedExperiment
Small RNA-seq data on 2406 samples from the Sequence Read Archive (SRA) processed using the miRge3 pipeline.
Read count matrix prepared and provided by authors of the study
Matthew N McCall, Min-Sik Kim, Mohammed Adil, Arun H Patil, Yin Lu, Christopher J Mitchell, Pamela Leal-Rojas, Jinchong Xu, Manoj Kumar, Valina L Dawson, Ted M Dawson, Alexander S Baras, Avi Z Rosenberg, Dan E Arking, Kathleen H Burns, Akhilesh Pandey, Marc Halushka (2017). Toward the human cellular microRNAome. Genome Research. 27(10):1769-1781.\ \ Patil AH, Baran A, Brehm ZP, McCall MN, Halushka MK. A curated human cellular microRNAome based on 196 primary cell types. Gigascience. 2022 Aug 25;11:giac083. doi: 10.1093/gigascience/giac083.
data(microRNAome) ## the microRNAome SummarizedExperiment object contains only one matrix ## in the assays field: a matrix of miRNA counts names(assays(microRNAome)) assays(microRNAome)$counts[1:3,1:3]data(microRNAome) ## the microRNAome SummarizedExperiment object contains only one matrix ## in the assays field: a matrix of miRNA counts names(assays(microRNAome)) assays(microRNAome)$counts[1:3,1:3]