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immApex

Tools for Adaptive Immune Receptor Sequence-Based Machine and Deep Learning

https://github.com/borchlab/immapex

Science Score: 26.0%

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    Scientific vocabulary similarity
    Low similarity (18.8%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Tools for Adaptive Immune Receptor Sequence-Based Machine and Deep Learning

Basic Info
Statistics
  • Stars: 12
  • Watchers: 1
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Created about 2 years ago · Last pushed 11 months ago
Metadata Files
Readme Changelog License

README.md

immApex

API for single-cell immune repertoire deep learning models

BioC status R-CMD-check Codecov test coverage <!-- badges: end -->

Introduction

Single-cell sequencing is now a integral tool in the field of immunology and oncology that allows researchers to couple RNA quantification and other modalities, like immune cell receptor profiling at the level of an individual cell. Towards this end, we developed the scRepertoire R package to assist in the interaction of immune receptor and gene expression sequencing. Further we developed models for embedding single-cell TCR sequences (Trex) and BCR sequences (Ibex) using convolutional neural networks. immApex is the API for preparing the sequence data for the current and future models in the scRepertoire ecosystem.

System requirements

immApex has been tested on R versions >= 4.0. Please consult the DESCRIPTION file for more details on required R packages - it is specifically designed to work with single-cell objects that have had BCR/TCRs added using scRepertoire. immApex has been tested on OS X and Linux platforms.

Installation

To run immApex, open R and install immApex from github:

r devtools::install_github("BorchLab/immApex")

or via Bioconductor with the 3.20 release

```r if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("immApex") ```

IMGT usage

IMGT is used as a reference for gene names and sequence information can be accessed via getIMGT(). Data from IMGT is under a CC BY-NC-ND 4.0 license. Please be aware that attribution is required for usage and it is the intent of IMGT to not allow derivative or commercial usage.

Usage/Demos

immApex should be able to be run in popular R-based single-cell workflows, including Seurat and Bioconductor/Single-Cell Experiment formats.

Quick Start

Check out this vignette for a quick start tutorial.

Bug Reports/New Features

If you run into any issues or bugs please submit a GitHub issue with details of the issue.

Any requests for new features or enhancements can also be submitted as GitHub issues.

Pull Requests are welcome for bug fixes, new features, or enhancements.

Owner

  • Name: BorchLab
  • Login: BorchLab
  • Kind: organization

GitHub Events

Total
  • Watch event: 3
  • Issue comment event: 2
  • Push event: 75
  • Pull request event: 10
  • Create event: 4
Last Year
  • Watch event: 3
  • Issue comment event: 2
  • Push event: 75
  • Pull request event: 10
  • Create event: 4

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 0
  • Total pull requests: 17
  • Average time to close issues: N/A
  • Average time to close pull requests: about 1 hour
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.47
  • Merged pull requests: 16
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 17
  • Average time to close issues: N/A
  • Average time to close pull requests: about 1 hour
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.47
  • Merged pull requests: 16
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
  • ncborcherding (17)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 2,301 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 7
  • Total maintainers: 1
bioconductor.org: immApex

Tools for Adaptive Immune Receptor Sequence-Based Machine and Deep Learning

  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 2,301 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 31.5%
Average: 42.4%
Downloads: 95.6%
Maintainers (1)
ncborch@gmail.com
Last synced: 11 months ago

Dependencies

.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v3 composite
  • actions/upload-artifact v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • R >= 4.0 depends
  • SingleCellExperiment * imports
  • dplyr * imports
  • hash * imports
  • httr * imports
  • keras * imports
  • matrixStats * imports
  • methods * imports
  • rvest * imports
  • stats * imports
  • stringi * imports
  • stringr * imports
  • tensorflow * imports
  • BiocStyle * suggests
  • ggplot2 * suggests
  • knitr * suggests
  • markdown * suggests
  • rmarkdown * suggests
  • scRepertoire * suggests
  • spelling * suggests
  • testthat * suggests
  • viridis * suggests