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geyser

https://github.com/davemcg/geyser

Science Score: 13.0%

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Last synced: 9 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: davemcg
  • License: cc0-1.0
  • Language: R
  • Default Branch: main
  • Size: 1.32 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 3
Created about 3 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License

README.md

geyser

Gene Expression displaY of SummarizedExperiment in R

Shiny-based app that uses the SummarizedExperiment data structure to flexibly plot gene (or transcript) expression by user-led sample grouping(s).

Solves the problem of "uh, here is a bunch of RNAseq data and I just want to quickly look at some gene expression patterns across arbitrary sample metadata labels without writing code"

Install

```

if needed: install.packages('remotes')

remotes::install_github("davemcg/geyser") ```

Quick Start

Note: Use tiny included SE object just to confirm the app functions for you library(geyser) load(system.file('extdata/tiny_rse.Rdata', package = 'geyser')) geyser(tiny_rse,'Test RSE')

Use recount3 to make a SE object

``` library(recount3) library(geyser) library(dplyr) humanprojects <- availableprojects() projinfo <- subset( humanprojects, project == "SRP107937" & projecttype == "datasources" ) rseSRP107937 <- createrse(projinfo) assay(rseSRP107937, "counts") <- transformcounts(rseSRP107937)

first tweak that glues the gene name onto the gene id in the row names

rownames(rseSRP107937) <- paste0(rowData(rseSRP107937)$genename, ' (', row.names(rseSRP107937), ')')

creates two new metadataa fields

colData(rseSRP107937)$tissue <- colData(rseSRP107937)$sra.sampletitle %>% stringr::strextract(.,'PRC|PR') colData(rseSRP107937)$disease <- colData(rseSRP107937)$sra.sampletitle %>% stringr::strextract(.,'AMD|Normal') geyser::geyser(rse_SRP107937, " geyser: SRP107937") ```

R Pseudocode to turn your count matrix and metadata into a SE object

```

YOUR METADATA ROWS NEED TO MATCH YOUR COUNT MATRIX COLUMNS

yourcountmatrix is an actual matrix (not a tibble!) with the row.names set to the gene

library(SummarizedExperiment) rse <- SummarizedExperiment(assays = list(counts = yourcountmatrix), colData = yourmetadata) colnames(rse) <- yourmetadata$sample_id ```

Related tools

The theme between these tools is that they do A LOT OF STUFF. geyser just does one thing - shows gene expression across your samples. Which, effectively, means less energy spent trying to figure out how to get started.

Owner

  • Name: David McGaughey
  • Login: davemcg
  • Kind: user
  • Location: Bethesda, MD
  • Company: NIH

Head, Bioinformatics Group, OGVFB, NEI, NIH

GitHub Events

Total
  • Push event: 3
  • Pull request event: 2
Last Year
  • Push event: 3
  • Pull request event: 2

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 77
  • Total Committers: 2
  • Avg Commits per committer: 38.5
  • Development Distribution Score (DDS): 0.247
Past Year
  • Commits: 5
  • Committers: 1
  • Avg Commits per committer: 5.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
David McGaughey m****y@g****m 58
David McGaughey d****g@u****m 19

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 0
  • Total pull requests: 6
  • Average time to close issues: N/A
  • Average time to close pull requests: less than a minute
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.17
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: less than a minute
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • 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
Pull Request Authors
  • davemcg (8)
Top Labels
Issue Labels
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Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 1,715 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 1
  • Total maintainers: 1
bioconductor.org: geyser

Gene Expression displaYer of SummarizedExperiment in R

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 1,715 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 30.3%
Average: 40.7%
Downloads: 91.9%
Maintainers (1)
mcgaughey@gmail.com
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • ComplexHeatmap * imports
  • DT * imports
  • SummarizedExperiment * imports
  • bslib >= 0.5.0 imports
  • dplyr * imports
  • ggbeeswarm * imports
  • ggplot2 * imports
  • htmltools * imports
  • magrittr * imports
  • shiny * imports
  • tibble * imports
  • tidyr * imports
  • tidyselect * imports
  • DESeq2 * suggests
  • airway * suggests
  • knitr * suggests
  • recount3 * suggests
  • rmarkdown * suggests
  • stringr * suggests
  • testthat >= 3.0.0 suggests