Code Ocean Apps

Code Ocean Apps is the dashboard where ready-to-use applications are available. These Apps can be used with or without customization and are regularly updated and added by the Science team.

The library consists of:

Genomics

• Delly Germline complete analysis

• Delly Somatic complete analysis

• FeatureCounts

• GATK RNAseq short variant discovery

• HOMER

• MacS3 Peak Calling

• Smoove complete analysis

Bulk Sequencing:

• BWA

• BWA Index

• BWA-MEM2

• Bowtie2

• Bowtie2 Index

• BWA-MEM2-Index

• Salmon

• STAR

• STAR Index

Utilities

• FastP

• Sambamba - Filter

• Sambamba - Remove Duplicates

• Trim Galore

Additional:

• ColabFold: Alphafold2

• FastQC

• Fetch Data with FFQ

• Img2Mol

• MLFlow - orchestration using S3

• MultiQC

• TensorBoard GPU

• DECIMER 2.0

NOTE: This dashboard has replaced the Open Science Library dashboard