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2021-09-23sample output dataAlexander Kabui
2021-09-23validate required outputAlexander Kabui
2021-09-23add mock test data for scriptAlexander Kabui
2021-09-23pass json file path as an argAlexander Kabui
2021-09-23pass other variables from user input for network constrAlexander Kabui
2021-09-23add rjson dependencyAlexander Kabui
2021-09-23load data from json file and and convert to dtAlexander Kabui
2021-09-22add init tests for call to scriptAlexander Kabui
2021-09-22add required wgcna dependencies to guix.scmAlexander Kabui
2021-09-22jsonify resultsAlexander Kabui
2021-09-22init endpoint tests for wgcnaAlexander Kabui
2021-09-16pylint fixesAlexander Kabui
2021-09-16Add WGCNA_SCRIT env to settingsAlexander Kabui
2021-09-16init tests for wgcnaAlexander Kabui
2021-09-16pass user input to call scriptAlexander Kabui
2021-09-16run cmd and add exception handlerAlexander Kabui
2021-09-16register wgcna blueprintAlexander Kabui
2021-09-16add initial endpoint for wgcnaAlexander Kabui
2021-09-16add function to compose and run wgcna scriptAlexander Kabui
2021-09-16function to parse form data and write to json fileAlexander Kabui
2021-09-15initial test file for wgcnaAlexander Kabui
2021-09-15init wgcna file to run r script and preprocess dataAlexander Kabui
2021-09-15remove golang package causing build failureAlexander Kabui
2021-09-15minor fixesAlexander Kabui
2021-09-15rename variables && delete debugsAlexander Kabui
2021-09-15Fetch IMAGE_DIR env and add img locationAlexander Kabui
2021-09-14remove debug statementsAlexander Kabui
2021-09-14function to generate rand str for imageAlexander Kabui
2021-09-14plot plotDendroAndColors and generate pngAlexander Kabui
2021-09-14construct gene co-expression network & module detectionAlexander Kabui
2021-09-14compute the softthreshholdAlexander Kabui
2021-09-14Checking data for excessive missing valuesAlexander Kabui
2021-09-14load the required data for analysisAlexander Kabui
2021-09-14init commit for wgcna scriptAlexander Kabui
2021-08-28README: updated install instructionsPjotr Prins
2021-08-28Add explanation of using a guix profilePjotr Prins
2021-08-28Fix issue that caused R/qtl to not use the first covariate when using stratif...zsloan
2021-08-26Added # permutations to verbose printzsloan
2021-08-20Minor correlation fixes (#36)...* fix key error for (*tissue_cor) tissue correlation * update tests for tissue correlation * rename speed_compute to fast_compute * pep8 formattingAlexander Kabui
2021-08-18Test the clustering...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/heatmap.py: Fix clustering bugs * tests/unit/computations/test_heatmap.py: Add new tests. Fix linting issues. Test and fix the clustering function. Muriithi Frederick Muriuki
2021-08-18Fix obvious linting errors...* Fix linting errors that do not change the function of the code. Muriithi Frederick Muriuki
2021-08-18Make child sequence a list...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Since the `slink` function assigns values to the `listcopy` variable and its children, this commit ensures that the sequence is a list to allow for the assignment. If the child-sequence is a tuple, that would lead to an exception. Muriithi Frederick Muriuki
2021-08-18Provide top-level `riset` key-value pair...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Provide the expected, top-level `riset` key-value pair and eliminate the redundant key-value pair. Muriithi Frederick Muriuki
2021-08-18Add tests and fix errors caught with tests...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/heatmap.py: fix errors * tests/unit/computations/test_heatmap.py: new tests Add new tests with the expected source data format, and expected results. Fix all errors that were caught by running the tests Muriithi Frederick Muriuki
2021-08-18Fix errors: add in missing parenthesis...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Call the `cursor.fetchone()` function to get results. Without the parenthesis, the code was trying to use the function itself as the results, which was a bug, and would lead to failure. Muriithi Frederick Muriuki
2021-08-18Initialise heatmap generation module...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/heatmaps/heatmaps.py: Initialise the module with some code to be used to test out plotly features on the command-line. * guix.scm: Add `python-plotly` and `python-pandas` as dependencies. Muriithi Frederick Muriuki
2021-08-16Merge pull request #32 from genenetwork/heatmap_decompose_db_retrieval...Heatmap decompose db retrievalBonfaceKilz
2021-08-12Fix linting errors...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Fix some errors caught by the linter. Muriithi Frederick Muriuki
2021-08-12Import missing definitions...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Import some missing definitions. Muriithi Frederick Muriuki
2021-08-11use normal function for correlation (#34)...* use normal function for correlation + rename functions * update test for sample correlation * use normal function for tissue correlation + rename functionsAlexander Kabui
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