R packages
Import/export
- pipette
- Input/output functions for biological data formats.
Data manipulation
- AcidPlyr
- A dplyr-like grammar for manipulation of S4 rectangular data classes, such as DFrame.
- syntactic
- Make syntactically valid names out of character vectors.
Visualization
- AcidPlots
- Functions for plotting genomic data.
RNA sequencing
- AcidExperiment
- Toolkit to extend the functionality of SummarizedExperiment.
- AcidGSEA
- Perform parameterized gene set enrichment analysis (GSEA) on multiple differential expression contrasts.
- DESeqAnalysis
- Toolkit for performing differential expression with DESeq2.
Single-cell RNA sequencing
- AcidSingleCell
- Toolkit for single-cell RNA-seq analysis that extends the functionality of SingleCellExperiment.
- Chromium
- Toolkit for 10X Genomics Chromium single cell data.
- pointillism
- Toolkit for single-cell RNA-seq clustering analysis.
Annotation databases
- AcidGenomes
- Toolkit for downloading and processing genome annotations.
- Cellosaurus
- Cellosaurus identifier mapping toolkit.
- EggNOG
- EggNOG database annotations.
- PANTHER
- PANTHER database annotations.
- WormBase
- Fetch Caenorhabditis elegans genome annotations from WormBase.
Infrastructure
- AcidBase
- Base functions imported by Acid Genomics packages.
- AcidCLI
- Command line interface helpers for Acid Genomics packages.
- AcidDevTools
- Toolkit for R package development.
- AcidGenerics
- S4 generic functions for Acid Genomics packages.
- AcidMarkdown
- Toolkit for extending the functionality of R Markdown.
- AcidRoxygen
- Shared roxygen2 documentation for Acid Genomics packages.
- AcidTest
- Reference data for Acid Genomics unit tests.
- basejump
- Toolkit for bioinformatics and R package development.
- goalie
- Assertive check functions for defensive R programming.
Source code is provided under the Apache 2.0 license.
© 2019-pres. Acid Genomics LLC.