Package: m6Aboost 1.19.0

You Zhou

m6Aboost: m6Aboost

This package can help user to run the m6Aboost model on their own miCLIP2 data. The package includes functions to assign the read counts and get the features to run the m6Aboost model. The miCLIP2 data should be stored in a GRanges object. More details can be found in the vignette.

Authors:You Zhou [aut, cre], Kathi Zarnack [aut]

m6Aboost_1.19.0.tar.gz
m6Aboost_1.19.0.zip(r-4.7)m6Aboost_1.19.0.zip(r-4.6)m6Aboost_1.19.0.zip(r-4.5)
m6Aboost_1.19.0.tgz(r-4.6-any)m6Aboost_1.19.0.tgz(r-4.5-any)
m6Aboost_1.19.0.tar.gz(r-4.7-any)m6Aboost_1.19.0.tar.gz(r-4.6-any)
m6Aboost_1.19.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
m6Aboost/json (API)

# Install 'm6Aboost' in R:

install.packages('m6Aboost', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/zarnackgroup/m6aboost/issues

On BioConductor:m6Aboost-1.19.0(bioc 3.24)m6Aboost-1.18.0(bioc 3.23)

sequencing epigenetics genetics experimenthubsoftware

4.48 score 3 stars 5 scripts 4 exports 142 dependencies

Last updated from:63cb5e5f01. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	270
linux-devel-x86_64	OK	425
source / vignettes	OK	386
linux-release-x86_64	OK	434
macos-release-arm64	OK	289
macos-oldrel-arm64	OK	270
windows-devel	OK	400
windows-release	OK	380
windows-oldrel	OK	375
wasm-release	OK	244

Exports:CtoTAssignment m6Aboost preparingData truncationAssignment

Dependencies:abind adabag AnnotationDbi AnnotationHub askpass BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocVersion Biostrings bit bit64 bitops blob BSgenome cachem caret cigarillo class cli clock codetools ConsRank cpp11 crayon curl data.table DBI dbplyr DelayedArray diagram digest doParallel dplyr e1071 ExperimentHub farver fastmap filelock foreach formatR futile.logger futile.options future future.apply generics GenomicAlignments GenomicRanges ggplot2 globals glue gower gtable gtools hardhat httr httr2 ipred IRanges isoband iterators jsonlite KEGGREST KernSmooth labeling lambda.r lattice lava lifecycle listenv lubridate magrittr MASS Matrix MatrixGenerics matrixStats memoise mime ModelMetrics nlme nnet numDeriv openssl parallelly pillar pkgconfig plyr png pROC prodlim progressr proxy purrr R6 rappdirs RColorBrewer Rcpp RCurl recipes reshape2 restfulr Rhtslib rjson rlang rlist rpart Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 scales Seqinfo shape snow SparseArray sparsevctrs SQUAREM stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect timechange timeDate tzdb utf8 vctrs viridisLite withr XML XVector yaml

Predicting m6A sites from miCLIP2 data with m6Aboost

Rendered fromm6AboosVignettes.Rmdusingknitr::rmarkdown

Last update: 2021-06-03
Started: 2021-05-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
CtoTAssignment for assigning the truncation read counts to the GRanges object with single nucleotide peaks	CtoTAssignment
m6Aboost for identify the m6A peaks from the miCILP2 data	m6Aboost
preparingData for the miCILP2 data	preparingData
truncationAssignment for assigning the truncation read counts to the GRanges object with single nucleotide peaks	truncationAssignment