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https://github.com/bioconductor-source/snifter

https://github.com/bioconductor-source/snifter

Science Score: 13.0%

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    CITATION.cff file
  • ✓
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    .zenodo.json file
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    DOI references
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    Low similarity (8.3%) to scientific vocabulary
Last synced: 9 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: bioconductor-source
  • Language: R
  • Default Branch: devel
  • Size: 507 KB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created almost 2 years ago · Last pushed almost 2 years ago
Metadata Files
Readme Changelog

README.Rmd 

---
output: md_document
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 8,
  fig.height = 6,
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# snifter

[![R build status](https://github.com/Alanocallaghan/snifter/workflows/R-CMD-check/badge.svg)](https://github.com/Alanocallaghan/snifter/actions)
[![BioC status](http://www.bioconductor.org/shields/build/release/bioc/snifter.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/snifter)



R binding for [openTSNE](https://opentsne.readthedocs.io/en/latest/index.html)
using [basilisk](https://bioconductor.org/packages/devel/bioc/html/basilisk.html).

## Example usage

Basic usage of the function returns a matrix of t-SNE coordinates.

```{r}
library("snifter")
set.seed(42)
m <- matrix(rnorm(20000), ncol = 20) 
snifter <- fitsne(m[-(1:2), ], random_state = 42L)
plot(snifter, pch = 19, xlab = "t-SNE 1", ylab = "t-SNE 2")
```

We can also project new points into an existing embedding.

```{r}
n <- 20
snifter <- fitsne(m[-(1:n), ], random_state = 42L)
plot(snifter, pch = 19, col = "black",
    xlab = "t-SNE 1", ylab = "t-SNE 2")
new <- project(snifter, m[1:n, ], old = m[-c(1:n), ])
points(new, pch = 19, col = "red")
```

Owner

  • Name: (WIP DEV) Bioconductor Packages
  • Login: bioconductor-source
  • Kind: organization
  • Email: maintainer@bioconductor.org

Source code for packages accepted into Bioconductor

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Dependencies

.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v3 composite
  • actions/upload-artifact v1 composite
  • grimbough/bioc-actions/setup-bioc v1 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • R >= 4.0.0 depends
  • assertthat * imports
  • basilisk * imports
  • irlba * imports
  • reticulate * imports
  • stats * imports
  • BiocStyle * suggests
  • ggplot2 * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat >= 3.0.0 suggests