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I believe the read depth chart is currently calculating the average coverage over the entire genome. This will yield a very small Y axis, so even if you zoom into an area where you know there's covera…
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...since @dodedic's CSV files are currently ~40MB in size, you might want to look into: [`scipy.sparse.save_npz`](https://docs.scipy.org/doc/scipy/reference/generated/scipy.sparse.save_npz.html#scipy-…
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scipy csr matrices have an implied value of zero for all non specified values. However this isn't being respected when converting between the two i.e:
```
from scipy.sparse import csr_matrix
from x…
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Hi,
I wonder if performing a bootstrap first on sparse sampling data and then conducting NCA would be a good approach for data statistical analysis?
Here are some references I found in the l…
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Use sparse matrix algebra when involving identity matrix arithmatics (I-A; A / x). Expected increase in performance as showed in #41.
- [ ] Check sparsity ratio for EXIOBASE data
- [ ] Investigate…
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In order to offer *physical data independence* to users, DAPHNE must be able to automatically decide the physical representation of a data object. In this context, the decision for a dense or a sparse…
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I'm running pycisTopic but `create_cistopic_object_from_fragments` has significant memory usage.
As has already been discussed (e.g. see https://github.com/aertslab/pycisTopic/issues/14), the main…
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Writing up a discussion with @ivirshup:
Scipy is moving away from their matrix API towards the array API (see note [here](https://docs.scipy.org/doc/scipy/reference/sparse.html)). Consequently, or…
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we need more efficient handling of sparse data. Thinking about sparseness for every data set is worse than just having algorithms which handle sparse data.
In xarray (https://docs.xarray.dev/en/sta…
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**Submitting author:** @annagraff (Anna Graff)
**Repository:** https://github.com/annagraff/densify
**Branch with paper.md** (empty if default branch): main
**Version:** v0.1.0
**Editor:** Pending
**R…