0 Important announcement | 1 Installation | 2 Obtaining the example NxtIRF genome and gene annotation files | 3 Obtaining the example BAM file dataset for SpliceWiz | 4 Obtaining the Mappability Exclusion BED files | 5 Accessing NxtIRFdata via ExperimentHub | 5 Information about the example BAM files | SessionInfo
Package: NxtIRFdata 1.18.0
Alex Chit Hei Wong
NxtIRFdata: Data for NxtIRF
NxtIRFdata is a companion package for SpliceWiz, an interactive analysis and visualization tool for alternative splicing quantitation (including intron retention) for RNA-seq BAM files. NxtIRFdata contains Mappability files required for the generation of human and mouse references. NxtIRFdata also contains a synthetic genome reference and example BAM files used to demonstrate SpliceWiz's functionality. BAM files are based on 6 samples from the Leucegene dataset provided by NCBI Gene Expression Omnibus under accession number GSE67039.
Authors:
NxtIRFdata_1.18.0.tar.gz
NxtIRFdata_1.18.0.tar.gz(r-4.7-any)NxtIRFdata_1.18.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
NxtIRFdata/json (API)
| # Install 'NxtIRFdata' in R: |
| install.packages('NxtIRFdata', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/alexchwong/nxtirfdata/issues
On BioConductor:NxtIRFdata-1.19.0(data/experiment 3.24)NxtIRFdata-1.18.0(data/experiment 3.23)
experimentdatapackagetypedatagenomernaseqdataexpressiondataexperimenthubdatapkg
Last updated from:f36b181dd8 (on RELEASE_3_23). Checks:3 NOTE, 1 OK. Indexed: no.
This is a data package. Data packages may be large and do not get checked across all platforms.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 151 | ||
| linux-devel | NOTE | 290 | ||
| source / vignettes | OK | 244 | ||
| linux-release | NOTE | 242 |
Exports:chrZ_genomechrZ_gtfexample_bamsget_mappability_exclusion
Dependencies:abindAnnotationDbiAnnotationHubaskpassBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydplyrExperimentHubfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesgluehttrhttr2IRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngpurrrR.methodsS3R.ooR.utilsR6rappdirsRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrswithrXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| NxtIRFdata: Data Package for SpliceWiz | NxtIRFdata-package chrZ_genome chrZ_gtf example_bams get_mappability_exclusion |