Package: brainflowprobes 1.19.0

Amanda Price

brainflowprobes: Plots and annotation for choosing BrainFlow target probe sequence

Use these functions to characterize genomic regions for BrainFlow target probe design.

Authors:Amanda Price [aut, cre], Leonardo Collado-Torres [ctb]

brainflowprobes_1.19.0.tar.gz
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brainflowprobes.pdf |brainflowprobes.html✨
brainflowprobes/json (API)
NEWS

# Install 'brainflowprobes' in R:

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

Bug tracker:https://github.com/lieberinstitute/brainflowprobes/issues

Datasets:

four_panels_example_cov - Example base-pair region coverage data
pd - A list of phenotype data.frames

On BioConductor:brainflowprobes-1.19.0(bioc 3.20)brainflowprobes-1.18.0(bioc 3.19)

bioconductor-package

7 exports 0.71 score 180 dependencies

Last updated 2 months agofrom:a4487f241e

Exports:brainflowprobes_cov check_pdf four_panels get_nearest_annotation get_region_cov plot_coverage region_info

Dependencies:abind AnnotationDbi AnnotationFilter AnnotationHub askpass backports base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocVersion biomaRt Biostrings biovizBase bit bit64 bitops blob broom broom.helpers BSgenome BSgenome.Hsapiens.UCSC.hg19 bslib bumphunter cachem checkmate cli clipr cluster codetools colorspace cowplot cpp11 crayon curl data.table DBI dbplyr DelayedArray derfinder derfinderHelper derfinderPlot dichromat digest doRNG dplyr ensembldb evaluate fansi farver fastmap filelock fontawesome forcats foreach foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges GenomicState GGally ggbio ggplot2 ggstats glue graph gridExtra gtable haven highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling labelled lambda.r lattice lazyeval lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme nnet openssl org.Hs.eg.db OrganismDbi patchwork pillar pkgconfig plogr plyr png prettyunits progress ProtGenerics purrr qvalue R6 rappdirs RBGL RColorBrewer Rcpp RCurl readr reshape2 restfulr Rhtslib rjson rlang rmarkdown rngtools rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex txdbmaker tzdb UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite vroom withr xfun XML xml2 XVector yaml zlibbioc

brainflowprobes user guide

Amanda Price

Rendered frombrainflowprobes-vignette.Rmdusingknitr::rmarkdownon Jun 16 2024.

Last update: 2023-05-07
Started: 2019-07-11

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Extract coverage data for a set of regions	brainflowprobes_cov
Check the PDF file	check_pdf
Plot expression coverage in four datasets for candidate probe sequences.	four_panels
Example base-pair region coverage data	four_panels_example_cov
Compute the nearest annotation to the annoated genes in brainflowprobes	get_nearest_annotation
Check or compute the region coverage from the datasets in brainflowprobes	get_region_cov
A list of phenotype data.frames	pd
Plot coverage in nuclear and cytoplasmic RNA for candidate probe sequences.	plot_coverage
Print relevant info about candidate probe sequence.	region_info