Acid Genomics
Tools for bioinformatics and functional genomics.
Shell configuration
- koopa
- Shell bootloader for bioinformatics.
Import/export
- pipette
- Pipette biological data in and out of R.
- AcidGenomes
- Toolkit for downloading and processing genome annotations.
- AcidPlyr
- A grammar of S4 class data manipulation.
- goalie
- Assertive check functions for defensive R programming.
- syntactic
- Make syntactically valid names out of character vectors.
Visualization
- AcidPlots
- Functions for plotting genomic data.
RNA sequencing
- DESeqAnalysis
- Toolkit for performing differential expression with DESeq2.
- AcidGSEA
- Parameterized fast gene set enrichment analysis (GSEA).
- AcidExperiment
- Toolkit to extend the functionality of SummarizedExperiment.
- bcbioRNASeq
- R package for bcbio RNA-seq analysis.
Single-cell RNA sequencing
- pointillism
- R package for for single-cell RNA-seq clustering analysis.
- Chromium
- Toolkit for 10X Genomics single-cell RNA-seq data.
- AcidSingleCell
- Toolkit for single-cell RNA-seq analysis that extends the functionality of
SingleCellExperiment.
- bcbioSingleCell
- R package for bcbio single-cell RNA-seq analysis.
Functional genomics
- DepMapAnalysis
- Cancer Dependency Map (DepMap) analysis toolkit (experimental).
- cBioPortalAnalysis
- Toolkit for performing queries on cBioPortal (experimental).
Annotation databases
- Cellosaurus
- Cellosaurus identifier mapping toolkit.
- EggNOG
- EggNOG database annotations.
- PANTHER
- PANTHER database annotations.
- WormBase
- C. elegans genome annotations from WormBase.
Source code is provided under the AGPLv3 license.
© 2019-pres. Acid Genomics LLC.