Download Databases for Local RNAseq Processing
  • For species "With a Reference Transcriptome", databases are Kallisto transcriptome index files for different species.
  • For species "Without a Reference Transcriptome", databases are ortholog databases from EcoOmicsDB, organized into different taxonomic groups. For more details, please visit Seq2Fun project page.
Species Accession ID Source Download
Homo sapiens (human) GCF_000001405 NCBI
Mus musculus (mouse) GCF_000001635 NCBI
Rattus norvegicus (rat) GCF_000001895 NCBI
Danio rerio (zebrafish) GCF_000002035 NCBI
Arabdopsis thaliana (thale cress) Araport11_genes Tair
Bos taurus (cow) GCF_002263795 NCBI
Caenorhabditis elegans (roundworm) GCA_000002985 NCBI
Coturnix japonica (Japanese quail) GCF_001577835 NCBI
Daphnia magna (water flea) GCA_001632505 NCBI
Drosophila melanogaster (fruit fly) GCA_000001215 Ensembl
Folsomia candida (springtail species) GCF_002217175 NCBI
Gallus gallus (chicken) GCF_000002315 NCBI
Homarus americanus (American lobster) GCA_018991925 NCBI
Hyalella azteca (freshwater shrimp) GCA_000764305 NCBI
Oncorhynchus mykiss (rainbow trout) GCF_013265735 NCBI
Pimephales promelas (fathead minnow) GCF_016745375 NCBI
Raphidocelis subcapitata (type of microalga) BDRX00000000 GenBank
Saccharomyces cerevisiae (yeast) GCF_000146045 NCBI
Schistosoma mansoni (type of blood fluke) GCA_000237925 NCBI
Creontiades dilutus (green mirid) De novo assembly NA
Lithobates pipiens (northern leopard frog) De novo assembly NA
Phalacrocorax auritus (double-crested cormorant) De novo assembly NA
Source Code
  • ExpressAnalystR GitHub repository (see installation instructions here)
  • Seq2Fun GitHub repository (see installation instructions here)
  • Web Framework: DropBox link (the source code is provided for transparency. It is not intended to run as production server which requires advanced system admin expertise to set up and to maintain).
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