Data

Tools

Indexes

Applications

Experiments

Open Source Science

SpliceWiz

SpliceWiz is an R package for exploring differential alternative splicing events in splice-aware alignment BAM files.

https://github.com/alexchwong/splicewiz

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 3 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.1%) to scientific vocabulary

Keywords from Contributors

bioconductor-packages grna-sequence
Last synced: 10 months ago · JSON representation

Repository

SpliceWiz is an R package for exploring differential alternative splicing events in splice-aware alignment BAM files.

Basic Info
  • Host: GitHub
  • Owner: alexchwong
  • License: other
  • Language: R
  • Default Branch: main
  • Size: 10.1 MB
Statistics
  • Stars: 20
  • Watchers: 1
  • Forks: 8
  • Open Issues: 12
  • Releases: 0
Created over 4 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License

README.md

SpliceWiz

SpliceWiz is an R package for exploring differential alternative splicing events in splice-aware alignment BAM files.

Table of Contents

  1. Documentation
    1. Bioconductor Release
    2. Bioconductor Devel
  2. Installation
    1. Enabling OpenMP (MacOS)
    2. Installation for Bioconductor (current release)
    3. Installation for Bioconductor (devel)
    4. Installing via GitHub
  3. Publication

Documentation

Bioconductor Release (Bioc 3.20 / R 4.4)

Bioconductor Landing Page (Release)

QuickStart Vignette (Release)

Reference Manual (Release)

Bioconductor Devel (future Bioc 3.21 / R 4.5)

Bioconductor Landing Page (Devel)

QuickStart Vignette (Devel)

Reference Manual (Devel)

Installation (Release - Bioc 3.20 / R 4.4)

Enabling OpenMP multi-threading (for MacOS users)

OpenMP is installed by default on Windows and Linux systems. For MacOS, OpenMP is not officially supported. To install SpliceWiz with OpenMP support, first install the libomp libraries via brew:

brew install libomp

On R (version >= 4.4) using Bioconductor version 3.20 (current release)

``` if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install(version = "3.20") BiocManager::valid() # checks for out of date packages

BiocManager::install("SpliceWiz") ```

On R-devel using Bioconductor devel (future 3.21)

``` if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install(version = "devel") BiocManager::valid() # checks for out of date packages

BiocManager::install("SpliceWiz") ```

Installing via GitHub

Reasons for installing via GitHub: * Using the latest development version on current release of Bioconductor - means you don't have to install Bioconductor devel * You are using Bioconductor version 3.16 or earlier

``` library("devtools") install_github("alexchwong/ompBAM")

To install the latest devel version, install from the "main" branch

install_github("alexchwong/SpliceWiz", "main", dependencies=TRUE) ```

Note that prior to Bioconductor versions 3.14 or earlier, you may need to retrieve Mappability files from https://github.com/alexchwong/SpliceWizResources

Publication

SpliceWiz is now published!

SpliceWiz: interactive analysis and visualization of alternative splicing in R

Owner

  • Name: Alex CH Wong
  • Login: alexchwong
  • Kind: user
  • Location: Centenary Institute
  • Company: Gene and Stem Cell Therapy Program

Research Officer

GitHub Events

Total
  • Issues event: 17
  • Watch event: 4
  • Issue comment event: 15
  • Push event: 3
  • Fork event: 1
Last Year
  • Issues event: 17
  • Watch event: 4
  • Issue comment event: 15
  • Push event: 3
  • Fork event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 663
  • Total Committers: 3
  • Avg Commits per committer: 221.0
  • Development Distribution Score (DDS): 0.006
Past Year
  • Commits: 417
  • Committers: 3
  • Avg Commits per committer: 139.0
  • Development Distribution Score (DDS): 0.01
Top Committers
Name Email Commits
alexchwong 8****g 659
J Wokaty j****y 2
J Wokaty j****y@s****u 2
Committer Domains (Top 20 + Academic)
sph.cuny.edu: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 40
  • Total pull requests: 41
  • Average time to close issues: 22 days
  • Average time to close pull requests: 2 days
  • Total issue authors: 33
  • Total pull request authors: 3
  • Average comments per issue: 3.25
  • Average comments per pull request: 0.05
  • Merged pull requests: 39
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 15
  • Pull requests: 1
  • Average time to close issues: 17 days
  • Average time to close pull requests: less than a minute
  • Issue authors: 14
  • Pull request authors: 1
  • Average comments per issue: 1.73
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • rezarahman12 (5)
  • t3h4nt1chr15t (3)
  • GimenaA (2)
  • mmilevskiy (2)
  • DarioS (2)
  • dksenthil (1)
  • ajblatnik (1)
  • Desertodunas (1)
  • BALASUNDAR30 (1)
  • jiaco (1)
  • droplet-lab (1)
  • anuradhareddi (1)
  • ZLS01 (1)
  • michael-mazzucco (1)
  • clydeugene (1)
Pull Request Authors
  • alexchwong (42)
  • pekkarr (2)
  • cparsania (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 8,255 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 11
  • Total maintainers: 1
bioconductor.org: SpliceWiz

interactive analysis and visualization of alternative splicing in R

  • Versions: 11
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 8,255 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Forks count: 15.3%
Average: 28.2%
Stargazers count: 33.2%
Downloads: 92.5%
Maintainers (1)
alexchwong.github@gmail.com
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • NxtIRFdata * depends
  • AnnotationHub * imports
  • BSgenome * imports
  • BiocFileCache * imports
  • BiocGenerics * imports
  • BiocParallel * imports
  • Biostrings * imports
  • DT * imports
  • DelayedArray * imports
  • DelayedMatrixStats * imports
  • GenomeInfoDb * imports
  • GenomicRanges * imports
  • HDF5Array * imports
  • IRanges * imports
  • R.utils * imports
  • RColorBrewer * imports
  • Rcpp >= 1.0.5 imports
  • S4Vectors * imports
  • SummarizedExperiment * imports
  • data.table * imports
  • fst * imports
  • genefilter * imports
  • ggplot2 * imports
  • grDevices * imports
  • heatmaply * imports
  • htmltools * imports
  • magrittr * imports
  • matrixStats * imports
  • methods * imports
  • ompBAM * imports
  • parallel * imports
  • patchwork * imports
  • pheatmap * imports
  • plotly * imports
  • progress * imports
  • rhandsontable * imports
  • rhdf5 * imports
  • rtracklayer * imports
  • rvest * imports
  • scales * imports
  • shiny * imports
  • shinyFiles * imports
  • shinyWidgets * imports
  • shinydashboard * imports
  • stats * imports
  • stringi * imports
  • tools * imports
  • utils * imports
  • DBI * suggests
  • DESeq2 * suggests
  • DoubleExpSeq * suggests
  • GO.db * suggests
  • Rsubread * suggests
  • crayon * suggests
  • edgeR * suggests
  • fgsea * suggests
  • knitr * suggests
  • limma * suggests
  • openssl * suggests
  • rmarkdown * suggests
  • splines * suggests
  • testthat >= 3.0.0 suggests
inst/htslib_version/DESCRIPTION cran
  • NxtIRFdata * depends
  • AnnotationHub * imports
  • BSgenome * imports
  • BiocFileCache * imports
  • BiocGenerics * imports
  • BiocParallel * imports
  • Biostrings * imports
  • DT * imports
  • DelayedArray * imports
  • DelayedMatrixStats * imports
  • GenomeInfoDb * imports
  • GenomicRanges * imports
  • HDF5Array * imports
  • IRanges * imports
  • R.utils * imports
  • RColorBrewer * imports
  • Rcpp >= 1.0.5 imports
  • S4Vectors * imports
  • SummarizedExperiment * imports
  • data.table * imports
  • fst * imports
  • genefilter * imports
  • ggplot2 * imports
  • grDevices * imports
  • heatmaply * imports
  • htmltools * imports
  • magrittr * imports
  • matrixStats * imports
  • methods * imports
  • ompBAM * imports
  • parallel * imports
  • patchwork * imports
  • pheatmap * imports
  • plotly * imports
  • progress * imports
  • rhandsontable * imports
  • rhdf5 * imports
  • rtracklayer * imports
  • rvest * imports
  • scales * imports
  • shiny * imports
  • shinyFiles * imports
  • shinyWidgets * imports
  • shinydashboard * imports
  • stats * imports
  • stringi * imports
  • tools * imports
  • utils * imports
  • DBI * suggests
  • DESeq2 * suggests
  • DoubleExpSeq * suggests
  • GO.db * suggests
  • Rsubread * suggests
  • crayon * suggests
  • edgeR * suggests
  • fgsea * suggests
  • knitr * suggests
  • limma * suggests
  • openssl * suggests
  • rmarkdown * suggests
  • splines * suggests
  • testthat >= 3.0.0 suggests