Package: primirTSS 1.31.0

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_1.31.0.tar.gz
primirTSS_1.31.0.zip(r-4.7)primirTSS_1.31.0.zip(r-4.6)primirTSS_1.31.0.zip(r-4.5)
primirTSS_1.31.0.tgz(r-4.6-any)primirTSS_1.31.0.tgz(r-4.5-any)
primirTSS_1.31.0.tar.gz(r-4.7-any)primirTSS_1.31.0.tar.gz(r-4.6-any)
primirTSS_1.31.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
primirTSS/json (API)

# 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-1.31.0(bioc 3.24)primirTSS-1.30.0(bioc 3.23)

immunooncology sequencing rnaseq genetics preprocessing transcription generegulation

4.48 score 2 scripts 6 exports 175 dependencies

Last updated from:28597fa812. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	354
linux-devel-x86_64	WARNING	511
source / vignettes	OK	415
linux-release-x86_64	WARNING	581
macos-release-arm64	WARNING	332
macos-oldrel-arm64	WARNING	409
windows-devel	WARNING	412
windows-release	WARNING	430
windows-oldrel	WARNING	407
wasm-release	OK	325

Exports:find_tss peak_join peak_merge plot_primiRNA run_primirTSSapp trans_cor

Dependencies:abind AnnotationDbi AnnotationFilter AnnotationHub askpass backports base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake BiocManager BiocParallel BiocVersion biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome BSgenome.Hsapiens.UCSC.hg38 bslib cachem caTools checkmate cigarillo cli cluster codetools colorspace commonmark cpp11 crayon curl data.table DBI dbplyr DelayedArray deldir dichromat digest dir.expiry DirichletMultinomial dplyr ensembldb evaluate farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GenomicScores ggplot2 glue gridExtra gtable gtools Gviz h5mread 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 mime nnet openssl otel phastCons100way.UCSC.hg38 pillar pkgconfig png prettyunits progress promises ProtGenerics purrr pwalign R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo seqLogo shiny snow sourcetools SparseArray stringi stringr SummarizedExperiment sys TFBSTools TFMPvalue tibble tidyr tidyselect tinytex UCSC.utils utf8 VariantAnnotation vctrs viridisLite withr xfun XML xml2 xtable XVector yaml

primirTSS

Rendered fromprimirTSS.Rmdusingknitr::rmarkdown

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