Analysis

Data and metadata

• http://data.cloud.refinery-platform.org/ - Refinery sample data store on S3
• https://drive.google.com/drive/folders/0B0k9NINSuqHPa1N1bEZLVzRYUzA
• https://s3.amazonaws.com/biodata - used by bcbio-nextgen
• CloudMan test data:
  • http://cloudman-test.s3.amazonaws.com/tests/rna/index.html
  • http://cloudman-test.s3.amazonaws.com/tests/chIP/index.html
  • http://cloudman-test.s3.amazonaws.com/tests/downsampled-workshop-data/index.html

Testing

• https://github.com/refinery-platform/sample-data
• https://github.com/parklab/refinery-platform/blob/develop/refinery/ui/source/sample-files/refinery-sample-metadata.tsv - tabular metadata sample
• rfc-test.zip - ISA archive for testing with the Refinery test workflows
• PCBC? - tabular

Chip-Seq

• Small mm9 data set (chr19)
• Transcription Factor Binding of p42 Isoform of C/EBPa (human)
• ChIP-Seq of C/EBPalpha 45 minutes post-induction with estradiol (human)
• Genome-wide maps of chromatin state in pluripotent and lineage-committed cells (mouse)
• Genome-wide maps of binding sites of Nanog-like and Mxtx2 in blastula stage zebrafish embryos (zebrafish)
• Transcription factor binding during intestinal cell differentiation [TFB] (human)

RNA-Seq

• ReCount (human, mouse, yeast, rat, worm, and fly)
• E-MTAB-3766 - Simulation-based assessment of differential transcript usage using RNA-seq data: a matter of counting (human and fly) - paired end
• E-MTAB-4119 - Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences (human) - paired end, chr1 only(?)
• RNA-seq HL60 (human) - paired end, private (note: 1A_HL60_lane6_read2.fastq.gz archive is corrupt - do not use)

Galaxy tools and workflows

Version control repos

• https://github.com/refinery-platform
• https://github.com/stemcellcommons
• https://bitbucket.org/stemcellcommons

Distribution repos

• https://testtoolshed.g2.bx.psu.edu/view/refinery-platform:
  • Refinery test workflow
• https://toolshed.g2.bx.psu.edu/view/refinery-platform:
  • FastQC workflow
• https://testtoolshed.g2.bx.psu.edu/view/stemcellcommons
• https://toolshed.g2.bx.psu.edu/view/stemcellcommons

Notes

All workflows have appropriate annotations for import into Refinery.