Package: primirTSS 1.25.0

Pumin Li

primirTSS: Prediction of pri-miRNA Transcription Start Site

A fast, convenient tool to identify the TSSs of miRNAs by integrating the data of H3K4me3 and Pol II as well as combining the conservation level and sequence feature, provided within both command-line and graphical interfaces, which achieves a better performance than the previous non-cell-specific methods on miRNA TSSs.

Authors:Pumin Li [aut, cre], Qi Xu [aut], Jie Li [aut], Jin Wang [aut]

primirTSS_1.25.0.tar.gz
primirTSS_1.25.0.zip(r-4.5)primirTSS_1.25.0.zip(r-4.4)primirTSS_1.25.0.zip(r-4.3)
primirTSS_1.25.0.tgz(r-4.4-any)primirTSS_1.25.0.tgz(r-4.3-any)
primirTSS_1.25.0.tar.gz(r-4.5-noble)primirTSS_1.25.0.tar.gz(r-4.4-noble)
primirTSS_1.25.0.tgz(r-4.4-emscripten)
primirTSS.pdf |primirTSS.html✨
primirTSS/json (API)
NEWS

# Install 'primirTSS' in R:

install.packages('primirTSS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ipumin/primirtss/issues

On BioConductor:primirTSS-1.25.0(bioc 3.21)primirTSS-1.24.0(bioc 3.20)

immunooncology sequencing rnaseq genetics preprocessing transcription generegulation

4.48 score 2 scripts 168 downloads 6 exports 186 dependencies

Last updated 2 months agofrom:dcff06d171. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 30 2024
R-4.5-win	WARNING	Nov 30 2024
R-4.5-linux	WARNING	Nov 30 2024
R-4.4-win	WARNING	Nov 30 2024
R-4.4-mac	WARNING	Nov 30 2024
R-4.3-win	WARNING	Nov 30 2024
R-4.3-mac	WARNING	Nov 30 2024

Exports:find_tss peak_join peak_merge plot_primiRNA run_primirTSSapp trans_cor

Dependencies:abind annotate AnnotationDbi AnnotationFilter AnnotationHub askpass backports base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocVersion biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome BSgenome.Hsapiens.UCSC.hg38 bslib cachem caTools checkmate cli clipr cluster CNEr codetools colorspace commonmark cpp11 crayon curl data.table DBI dbplyr DelayedArray deldir dichromat digest DirichletMultinomial dplyr ensembldb evaluate fansi farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GenomicScores ggplot2 glue GO.db gridExtra gtable gtools Gviz HDF5Array highr Hmisc hms htmlTable htmltools htmlwidgets httpuv httr httr2 interp IRanges isoband JASPAR2018 jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice latticeExtra lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme nnet openssl phastCons100way.UCSC.hg38 pillar pkgconfig plogr plyr png poweRlaw pracma prettyunits progress promises ProtGenerics purrr pwalign R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl readr reshape2 restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales seqLogo shiny snow sourcetools SparseArray stringi stringr SummarizedExperiment sys TFBSTools TFMPvalue tibble tidyr tidyselect tinytex tzdb UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite vroom withr xfun XML xml2 xtable XVector yaml zlibbioc

primirTSS

Rendered fromprimirTSS.Rmdusingknitr::rmarkdownon Nov 30 2024.

Last update: 2018-09-07
Started: 2018-07-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Predict TSSs of miRNA	find_tss
Integrate H3K4me3 data and Pol II data.	peak_join
Merge adjacent peaks within H3K4me3 or Pol II data.	peak_merge
Plot the result of prediction for miRNA	plot_primiRNA
primirTSS: Search for putative TSSs of miRNA	primirTSS
Predict TSSs of miRNA using a graphical web interface.	run_primirTSSapp
transform one hg coordinates to another	trans_cor