Package: snapcount 1.25.0

Rone Charles

snapcount: R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts

snapcount is a client interface to the Snaptron webservices which support querying by gene name or genomic region. Results include raw expression counts derived from alignment of RNA-seq samples and/or various summarized measures of expression across one or more regions/genes per-sample (e.g. percent spliced in).

Authors:Rone Charles [aut, cre]

snapcount_1.25.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
snapcount/json (API)

# Install 'snapcount' in R:

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

Bug tracker:https://github.com/langmead-lab/snapcount/issues

On BioConductor:snapcount-1.25.0(bioc 3.24)snapcount-1.24.0(bioc 3.23)

coverage geneexpression rnaseq sequencing software dataimport

5.36 score 3 stars 19 scripts 26 exports 36 dependencies

Last updated from:ad069496bd. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	203
linux-devel-x86_64	NOTE	475
source / vignettes	OK	308
linux-release-x86_64	NOTE	457
macos-release-arm64	NOTE	348
macos-oldrel-arm64	NOTE	364
windows-devel	NOTE	377
windows-release	NOTE	354
windows-oldrel	NOTE	388
wasm-release	OK	173

Exports:Compilation Coordinates from_url get_column_filters get_compilation get_coordinate_modifier get_regions get_row_filters get_sids junction_inclusion_ratio junction_intersection junction_union percent_spliced_in query_exon query_gene query_jx QueryBuilder set_column_filters set_compilation set_coordinate_modifier set_regions set_row_filters set_sids shared_sample_counts tissue_specificity uri_of_last_successful_request

Dependencies:abind askpass assertthat Biobase BiocGenerics cli curl data.table DelayedArray generics GenomicRanges glue httr IRanges jsonlite lattice lifecycle magrittr Matrix MatrixGenerics matrixStats mime openssl purrr R6 rlang S4Arrays S4Vectors Seqinfo SparseArray stringi stringr SummarizedExperiment sys vctrs XVector

snapcount vignette

Rendered fromsnapcount_vignette.Rmdusingknitr::rmarkdown

Last update: 2020-12-07
Started: 2019-06-17

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
snapcount: an R package for interfacing with Snaptron	snapcount-package snapcount
Enum for Snaptron compilations	Compilation
Enum for Snaptron Coordinate modifiers	Coordinates
Constructs a 'QueryBuilder' object from the given url	from_url
Get or set sample-related contraints for query	get_column_filters set_column_filters
Get or set query compilation	get_compilation set_compilation
Get or set coordinate modifiers for the query.	get_coordinate_modifier set_coordinate_modifier
Get or set query regions	get_regions set_regions
Get or set range-related contraints for query	get_row_filters set_row_filters
Get or set query sample ids	get_sids set_sids
Relative measure of splice variant usage similar to PSI that allows for 2 arbitrarily defined groups of junctions (not limited to cassette exons).	junction_inclusion_ratio
Get the intersection of junctions from 2 or more compilations which are on the same reference	junction_intersection
Get the union of junctions from 2 or more compilations which are on the same reference	junction_union
Relative measure of splice variant usage, limited currently to cassette exon splice variants	percent_spliced_in
Query Junctions/Genes/Exons	query_exon query_gene query_jx
Construct a QueryBuilder object given a compilation and one or regions.	QueryBuilder
Shared Sample Count (SSC): counts total number of samples in which 2 different junctions both occur in.	shared_sample_counts
Tissue Specificity (TS): produces a list of samples with their tissues marked which either contain queried junctions (1) or not (0); can be used as input to significance testing methods such as Kruskal-Wallis to look for tissue enrichment (currently only works for the GTEx compilation).	tissue_specificity
Return the URI of the last successful request to Snaptron	uri_of_last_successful_request