Package: snapcount 1.19.0

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]

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snapcount.pdf |snapcount.html✨
snapcount/json (API)
NEWS

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

Peer review:

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

On BioConductor:snapcount-1.19.0(bioc 3.21)snapcount-1.18.0(bioc 3.20)

coveragegeneexpressionrnaseqsequencingsoftwaredataimport

5.16 score 3 stars 12 scripts 183 downloads 26 exports 39 dependencies

Last updated 23 days agofrom:975103765f. Checks:OK: 2 NOTE: 2 WARNING: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winWARNINGOct 31 2024
R-4.5-linuxNOTEOct 31 2024
R-4.4-winWARNINGOct 31 2024
R-4.4-macNOTEOct 31 2024
R-4.3-winWARNINGOct 31 2024
R-4.3-macOKOct 31 2024

Exports:CompilationCoordinatesfrom_urlget_column_filtersget_compilationget_coordinate_modifierget_regionsget_row_filtersget_sidsjunction_inclusion_ratiojunction_intersectionjunction_unionpercent_spliced_inquery_exonquery_genequery_jxQueryBuilderset_column_filtersset_compilationset_coordinate_modifierset_regionsset_row_filtersset_sidsshared_sample_countstissue_specificityuri_of_last_successful_request

Dependencies:abindaskpassassertthatBiobaseBiocGenericsclicrayoncurldata.tableDelayedArrayGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrIRangesjsonlitelatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpurrrR6rlangS4ArraysS4VectorsSparseArraystringistringrSummarizedExperimentsysUCSC.utilsvctrsXVectorzlibbioc

snapcount vignette

Christopher Wilks

Rendered fromsnapcount_vignette.Rmdusingknitr::rmarkdownon Oct 31 2024.

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

Readme and manuals

Help Manual

Help pageTopics
snapcount: an R package for interfacing with Snaptronsnapcount-package snapcount
Enum for Snaptron compilationsCompilation
Enum for Snaptron Coordinate modifiersCoordinates
Constructs a 'QueryBuilder' object from the given urlfrom_url
Get or set sample-related contraints for queryget_column_filters set_column_filters
Get or set query compilationget_compilation set_compilation
Get or set coordinate modifiers for the query.get_coordinate_modifier set_coordinate_modifier
Get or set query regionsget_regions set_regions
Get or set range-related contraints for queryget_row_filters set_row_filters
Get or set query sample idsget_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 referencejunction_intersection
Get the union of junctions from 2 or more compilations which are on the same referencejunction_union
Relative measure of splice variant usage, limited currently to cassette exon splice variantspercent_spliced_in
Query Junctions/Genes/Exonsquery_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 Snaptronuri_of_last_successful_request