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feat(data): generate transcriptome db and simulate deterministic data #537

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feat(data): generate transcriptome db and simulate deterministic data #537

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@cameronraysmith cameronraysmith commented Apr 1, 2024 •
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deps(pyproject): add bioinformatics group
70e7a2f 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
deps(nix): add overrides for bioinformatics group
72a4f22 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
feat(scripts): draft extraction of gene length and polyA motif counts
b35c55d 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
chore(lint): changelog
07ad321 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith cameronraysmith added enhancement New feature or request skip-ci Skip CI workflow labels Apr 1, 2024
@cameronraysmith cameronraysmith self-assigned this Apr 1, 2024
@cameronraysmith
fix(gitignore): database files
092deee 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(pyproject): omit scripts
55e9311 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
feat(analysis): create module to generate transcriptome properties da…
4fe27ae 
…tabase

Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(scripts): update transcript analysis
9594ab9 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith cameronraysmith removed the skip-ci Skip CI workflow label Apr 1, 2024
@cameronraysmith cameronraysmith added this to the 0.2.x milestone Apr 1, 2024
This was linked to issues Apr 1, 2024
plot input data summary #536
Open
support generation of a transcriptome properties database #538
Closed
@cameronraysmith
fix(analysis): log warning rather than raising error on lazy imports
fa834d2 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(analysis): use forward type hint for lazy import
436e526 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
deps(pyproject): include pyarrow, polars, ibis
4b41423 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
chore(requirements): sync pyproject
a791553 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
chore(conda): sync pyproject
c57f517 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(analysis): isolate pyensembl lazy import
ea55ab8 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(analysis): allow PathLike in transcriptome properties
a6384a9 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
feat(tests): add tests for transcriptome properties module
2a3e19c 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
chore(bazel): update lock
043ba01 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(flake): exclude tests requiring pyensembl
a322b8e 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(pyproject): default to exclude tests that require pyensembl
cbd905e 
this is only due to:

- the expectation of excessive time required to load the database on uninitialized CI systems
- relative infrequency with which this module needs to be executed given the ability to used cached copies of the database
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(gitignore): ignore ensembl cache directory
920cd20 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
feat(io): add async ensembl query and cache
997169f 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
feat(io): add async ensembl batch query and cache
2b15bf6 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
feat(io): add data fetch interface
2afa701 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
feat(models): add plot_sample_trajectories function
56eaed3 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(vscode): use basic project-manager
d73df90 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(vscode): add db client
23e0f00 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(models): update plot_sample_trajectories styling
a8291ae 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
test(models): add failing test for refactored `solve_model_for_all_ge…
2f02fa1 
…nes_cells`

Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(models): refactor solve_model_for_all_genes_cells from model
89de821 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(models): remove solve_model_for_all_genes_cells refactor TODO c…
8593da0 
…omment

Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(models): multiple concrete dims examples
bc5a254 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
test(models): add test for sort_times_over_all_cells
5421c1b 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(models): use log-normal likelihood
580d2ef 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
chore(nbs): add include-code-files extension
e2974d0 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
chore(nbs): init rrv
05b433e 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
nit(models): rename sample_y to sample_data
15f2425 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(models): remove redundant Result container for plot_sample_trajec…
b7ca6e0 
…tories

Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(models): plot single timepoint data as vectorized series
6dd2256 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(models): remove result wrapping from save_inference_plots
0aae2fe 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
feat(models): add plot_sample_trajectories_with_percentiles
f661696 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(models): refactor plot_trajectory_with_percentiles to work with m…
b02d816 
…ultiple timepoints per cell

Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
test(models): parameterize tests over single and multiple timepoint d…
7e42427 
…ata sets

Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(bazel): separate small and medium test modules
6186da2 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(models): compute all kwargs inside plot_sample_trajectories_with_…
df611a2 
…percentiles

Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(models): return all indices from sort_times_over_all_cells
91c13ab 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
test(models): add tests for plot_sample_phase_portraits
f332a4c 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
feat(models): add plot_sample_phase_portraits
e136293 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(models): separately normalize plot_sample_phase_portraits colorba…
d4ab537 
…r for linear and log

Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
fix(models): change logger from warning to debug
0221974 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
feat(nbs): update references
1c93eb6 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
feat(nbs): add inference plots to concepts
38b61ef 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
feat(nbs): add inference plots to rrv
44b915a 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
@cameronraysmith
chore(nbs): update freeze lock
c58a8f4 
Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>
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