0.0.0

[gfudenberg]

TODO

• [ ] migrate code to download data elsewhere in cooltools (e.g. lib.io)

Notebooks:

i/o

• [ ] #6

pairtools-walkthrough:

• [ ] map
• [ ] parse
• [ ] sort
• [ ] dedup
• [ ] stats
• [ ] discussion of artefacts?..
• [ ] cooler aggregation, balancing, zoomify

viz:

• [ ] higlass integration
• [ ] examples of translocations, other organisms (yeast)
• [ ] 45° rotated heatmap plotting (see insulation notebook)
• [ ] sample_cooler() ?

contacts_vs_distance:

• [ ] trans expected: modify example HFF cooler to have 3 chrms
• [ ] save to file

compartments_and_saddles

• [x] saddle.saddleplot, saddle.saddle_strength
• [ ] need to re-work to put the discussion of digitization after the simple example, since that is now hidden from the user
  • [ ] TBD: download fasta in ipynb or provide pre-binned GC content?
• [ ] #21

insulation_and_boundaries

• [x] Compute insulation, find peaks, visualize w/ map
• [x] pileup/stackup of CTCF ChIP-Seq coverage at boundaries
• [x] boundary filtering, thresholding based on CTCF

pileup_CTCF_boundaries

• [x] everything! (On-diagonal pileups at CTCF ChIP and called boundaries, ..)
• [x] on-diagonal pileups at CTCF peaks
• [x] off-diagonal pileups between CTCF peaks
• [ ] adaptive coarsegrain adaptation for pileups ?
• [ ] average Rabl configuration ?

dots_and_apa:

• [ ] everything! (Dot calling, visualize w/ map, aggregate pileups, pair of CTCF pileups)

also see https://github.com/open2c/cooltools/issues/312

[gfudenberg]

the viz notebook should print the c.bins()[:3] somewhere at the start of the balancing section, and then say aha the weights column is present, this cooler has been balanced done

[gfudenberg]

added viz notebook should also show an unbalanced matrix in the balancing section, otherwise its not very clear why balancing is relevant.

Q: should this link to cooler-binder (https://github.com/open2c/cooler-binder/blob/master/cooler_api.ipynb), or is that deprecated cc @nvictus ?

[gfudenberg]

maybe good to plot an observed/expected contact map in either contacts_vs_distance, viz, or compartments_saddles?