Salsa: An R package of data mining facilities for Capsicum gene expression profiles

Salsa is an auto-contained R package with data and functions to explore the transcriptome of 12 chili pepper (Capsicum annuum L.) accessions during fruit development. Data consist of curated gene expression profiles for more than 29000 genes sampled every ten days from 0 to 60 Days After Anthesis (DAA), incorporating also gene identification plus Gene Ontology (GO) annotations. Functions include extensive resources for expression pattern searching and plotting facilities, GO enrichment analysis as well as methods to evaluate expression pattern differences in sets of genes and accessions.

Data were obtained from twelve chili pepper accessions, six domesticated, four wild and two F1 crosses. RNA-Seq experiments were performed with fruits from each accession at 7 different times after anthesis. Additionally, samples of seedlings from two accessions were evaluated. The data set is comprised by 179 samples, that in total have more than 3 billion reads map to the Capsicum annuum genome. NCBI Gene Expression Omnibus (GEO) deposit entitled "Chili pepper RNA-Seq data for fruit development in a set of accessions"; see GEO record at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE165448

Details of the methods employed in Salsa, as well as examples of data mining using the package are presented in the paper "A method to analyze time expression profiles demonstrated in a database of chili pepper fruit development". Please cite that paper when using the package.

Data in Salsa, using a draft of the package, has been published in Plants  2021, 10, 585: Transcriptome Analyses throughout Chili Pepper Fruit Development Reveal Novel Insights into the Domestication Process and also in Int. J. Mol. Sci. 2021, 22(5), 2229: Genome-Wide Identification and Analysis of the MYB Transcription Factor Gene Family in Chili Pepper (Capsicum spp.). This research was funded by the Consejo Nacional de Ciencia y Tecnología, México (Conacyt) project number 1570.

In this version (0.5) the package includes two new data frames:
"library.desc" - Description of all 179 RNA-Seq libraries deposited in GEO and
"readcounts" - Raw number of reads for each gene at each RNA-Seq library.