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.

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.