* initial cut at backed mode
* make flask multithreading conditional on debug flag
* update X access to support backed mode
* lint
* improve help message for backed mode
* fix tests
* add MatrixProxy to normalize supported matrix types
* add FAQ entry for --backed
* remove use of matrix.T
* clean up
* add ability to disable diffexp from CLI; add hueristic to detect likely slow diffexp calculation, and warn user
* fix tests
* do not print diffexp speed warning if diffexp is disabled
* tweak wording of diffexp speed messages
* add FAQ entry on --disable-diffexp
* revise heuristic for warning about slow diffexp
* use quick tooltip delay on diffexp button
* initial commit of URL support for launch
* lint
* modify tests to use new data locator
* add locator unit tests
* fix typo in faq
* more lint
* update faq per PR review
* Update example datasets w/ pbmc3k and tabula muris
* Add `prepare` overview and example
* Add S3 data links
* Incorporate PR feedback & copyedits
* Switch to letter pointers
* unix line endings
* path
* improve column access speed for sparse matrices
* add FAQ entry about data format performance
* add note about using --sparse flag for prepare command
* clean up for PR review
* Update docs/faq.md
Co-Authored-By: bkmartinjr <bruce@chanzuckerberg.com>
* improvements to big data faq
* Added PR guidelines
Added document to cover guidelines for creating, reviewing and merging PRs.
* fixed typo
* another typo
* grammar
* Remove 5's title
The subheading is clearer as a top-level
* add cutoff for low expression genes in topN selection
* remove debugging printfs
* change cli param name for diffexp cutoff
* change CLI param name
* second try at diffexp - using lfc sort with pval cutoff
* use lfc cutoff
* update comments to match code; cap p-value adjustment to max of 1
* lint
* explain diffexp in readme
* add link
* add diffexp-lfc-cutoff to test config
* update test to match revised diffexp spec
* fix latent bug in GET arg handling that was breaking tests
* lint
* comment cleanup
* fix variance overestimation so it is symmetric
* lint
lots of updates to the readme to: improve scientific and technical clarity, reflect all recent changes to the CLI (especially the addition of prepare), reflect all recent changes to our installation, improve explanation of how to handle a few different kinds of data, and expand instructions on contributing and developing
* new diffexp REST API spec
* new diffexp REST API; faster diffexp and dataframe slicing
* first draft of fast diffexp
* convert variance calculation to two-pass method
* lint
* update front-end use of API
* fix typo in spec
* disable content compression
* catch index filter format errors
* clean up of dead code
* resolve PR review comments
