This repository has various annotation resources for different fungal genomes I have worked on. One can easily create these resources on their own using R packages like AnnotationForge, GenomicFeatures etc.
OrgDb packages: To prepare OrgDb package for an organism, gene information, GO assignment, KEGG pathway data was extracted from various public domain databases like AspGD, CGD, FunigDB, NCBI etc. This curated data was used with R function AnnotationForge::makeOrgPackage() to create OrgDb package. One can store different form of information for each gene in OrgDb package and once created, can easily extract the information using AnnotationDbi::select() function. This orgDb package can be used in GO enrichment analysis using clusterProfiler package.
TxDb packages: Most updated GFF or GTF file was obtained for organism of interest from public domain databases. All the TxDb packages were created using GenomicFeatures::makeTxDbFromGFF() function in R. Various Bioconductor R packages require a TxDb object of an organism for data analysis. See here for the details.
BSgenome packages: This package holds the FASTA sequence data in form of a R package object. BSgenome object allows easy manipulation of sequence data using R. One can imagine its function similar to samtools package. BioConductor version 3.12 onwards do not create BSgenome package from .2bit files if the genome is not NCBI or UCSC genome assembly.
topGO mapping files: OrgDb pacakge created for each organism in previous step was used to extract gene to GO assignment table. This table was saved in tabular file which is used by GO enrichment package topGO.
- OrgDb package:
org.AFumigatus.Af293.eg.db - TxDb package:
TxDb.Afumigatus.Af293.AspGD.GFF - BSgenome package:
BSgenome.Afumigatus.Af293.AspGD - Gene to GO mapping file for
topGOpackage: topGO_mapping
- OrgDb package:
org.AFumigatus.A1163.eg.db - TxDb package:
TxDb.Afumigatus.A1163.AspGD.GFF - BSgenome package:
BSgenome.Afumigatus.A1163.AspGD - Gene to GO mapping file for
topGOpackage: topGO_mapping
- OrgDb package:
org.Anidulans.FGSCA4.eg.db - TxDb package:
TxDb.Anidulans.FGSCA4.AspGD.GFF - BSgenome package:
BSgenome.Anidulans.FGSCA4.AspGD - Gene to GO mapping file for
topGOpackage: topGO_mapping
- OrgDb package:
org.Calbicans.SC5314.eg.db - TxDb package:
TxDb.Calbicans.SC5314.CGD.GFF - BSgenome package:
BSgenome.CAlbicans.SC5314.A21.CGD - Gene to GO mapping file for
topGOpackage: topGO_mapping
- OrgDb package:
org.Cauris.B8441.eg.db - TxDb package:
TxDb.Cauris.B8441.GFF - BSgenome package:
BSgenome.Cauris.B8441 - Gene to GO mapping file for
topGOpackage: topGO_mapping
License: GPL v2