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    You are using the free version of Circa
    • What's new in Circa
      February 21, 2025

      You can now explicitly set the min and max for the y-axis scale for all tracks with a "y" role, i.e. scatter, line, area, bars, and CNV.

      By default, min and max for the y-axis scale is set from the data's actual min and max values. That default behavior is still the same, but now you can choose to override those values.

      Override y-axis min/max illustration

      January 15, 2025

      Added a new gallery example showing genome-to-genome alignments and how to achieve a perfect mirrored view in Circa:

      January 15, 2025

      You can now customize how chromosome names are displayed using the "pretty_name" field in Setup. See documentation for more details.

      Pretty names illustration

      December 18, 2024

      Automatically deduplicate chromosomes during Setup by keeping only the copy of each chromosome with the largest "size". This can be useful if you don't already have a list of how long your chromosomes (or other sequences) are but do have some data like coverage with bins that end where the chromosomes end. Just load that data in the Setup CSV/TSV file section and choose the bin end coordinates as size like below:

      Deduplicate chromosomes by largest size

      December 17, 2024

      You can now delete all tracks associated with a data file.

      Remove dataset with tracks

      December 10, 2024

      Add pin style for the 'text' track type to allow showing text without overlapping.

      Non-overlapping text pins

      October 28, 2024

      Chromosomes can now be flipped to enable better comparisons between two genomes/haplotypes. Read more here.

      Flipped chromosomes

      October 14, 2024

      All colors now have copy-pastable hex codes:



      The gallery also features a new plot of RNA-seq differential expression:

Circa

Gallery

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Tutorial

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Structural variants & long-read sequencing in cancer
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RNA-Seq differential expression with DESeq2
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Genome alignments & homology with MUMmer4
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Copy-number variations and translocations in cancer
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Genome assembly and synteny in plants
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Genome assembly and synteny in wasps
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Plasmid features from bacterial genomes
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Bacterial genome alignments
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How to: Color by column

Coloring tracks by structural variant type

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How to: Copy number ideas

Many ways to show copy number data in Circa

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How to: Heatmap ideas

Several track types with continuous color scales

Documentation
  • Supported input files
  • Supported track types
  • Data Mapper: Connecting data to a track
  • Chromosome name matching
  • Customizing chromosome names
  • Flipping chromosomes and mirroring genomes
  • Install Circa as an app
  • Data privacy
  • Register your license key