| 697c5d8 | Guillaume Dumas | 27 March 2020, 15:51:32 UTC | Merge pull request #43 from ntraut/master Use numpy for computing propagation | 27 March 2020, 15:51:32 UTC |
| 2b57821 | Nicolas Traut | 27 March 2020, 09:40:56 UTC | Use numpy for computing propagation | 27 March 2020, 09:44:04 UTC |
| d628ebc | Guillaume DUMAS | 27 February 2020, 18:01:28 UTC | Correct COO/CSP sparse matrix bug | 27 February 2020, 18:01:28 UTC |
| c2c2181 | 0m1n0 | 27 February 2020, 17:01:46 UTC | Merge pull request #42 from 0m1n0/master Addition of the choice between launching the code in a one-time or by split steps | 27 February 2020, 17:01:46 UTC |
| 91e25d4 | 0m1n0 | 27 February 2020, 16:54:39 UTC | addition of the choice between launching the code in a one-time ("full_step") run or in three parts: "preprocessing", "bootstrap", "clustering" | 27 February 2020, 16:54:39 UTC |
| d8beb3d | 0m1n0 | 27 February 2020, 16:48:42 UTC | Merge branch 'master' of https://github.com/0m1n0/stratipy * 'master' of https://github.com/0m1n0/stratipy: Update README.md Versionning README.md Update to version 0.8 | 27 February 2020, 16:48:42 UTC |
| 322e8c4 | 0m1n0 | 27 February 2020, 16:48:11 UTC | not used comments removed | 27 February 2020, 16:48:11 UTC |
| 6355fdd | 0m1n0 | 27 February 2020, 16:47:32 UTC | print function with flush=True | 27 February 2020, 16:47:32 UTC |
| 26cc463 | 0m1n0 | 27 February 2020, 16:46:13 UTC | variable name changed: "patients" -> "Individuals" | 27 February 2020, 16:46:13 UTC |
| d88d881 | Guillaume Dumas | 09 December 2019, 15:09:57 UTC | Update setup.py | 09 December 2019, 15:09:57 UTC |
| 330bd4f | 0m1n0 | 09 December 2019, 11:54:39 UTC | Merge pull request #41 from 0m1n0/master Version release | 09 December 2019, 11:54:39 UTC |
| b6ba4da | 0m1n0 | 09 December 2019, 10:59:04 UTC | Update README.md Version release with DOI from data archiving tool Zenodo (2nd try) | 09 December 2019, 10:59:04 UTC |
| 54a2e7d | 0m1n0 | 09 December 2019, 10:56:31 UTC | Merge branch 'master' into master | 09 December 2019, 10:56:31 UTC |
| cc3ec8c | 0m1n0 | 09 December 2019, 10:49:55 UTC | Versionning README.md Version release with DOI from data archiving tool Zenodo | 09 December 2019, 10:49:55 UTC |
| 12ccb5f | Guillaume Dumas | 05 December 2019, 11:51:42 UTC | Update to version 0.8 | 05 December 2019, 11:51:42 UTC |
| 8182124 | 0m1n0 | 05 December 2019, 10:16:11 UTC | Merge pull request #39 from 0m1n0/master QN, alpha, propagation | 05 December 2019, 10:16:11 UTC |
| bccbf7b | 0m1n0 | 05 December 2019, 10:10:15 UTC | from binary to weighed mutation profile, based on observed/expected score of gnomAD | 05 December 2019, 10:10:15 UTC |
| 705b98a | 0m1n0 | 05 December 2019, 10:09:07 UTC | only one iteration of propagation, alpha fixed by PPI network edge number | 05 December 2019, 10:09:07 UTC |
| 8737509 | 0m1n0 | 05 December 2019, 10:07:57 UTC | PPI network data formatting cleaned | 05 December 2019, 10:07:57 UTC |
| 0793e21 | 0m1n0 | 05 December 2019, 10:07:03 UTC | variable name changed: patient -> individual | 05 December 2019, 10:07:03 UTC |
| 1ed217b | 0m1n0 | 27 May 2019, 14:34:00 UTC | individual selection with Admixture model | 27 May 2019, 14:34:00 UTC |
| 64a1113 | 0m1n0 | 27 May 2019, 14:33:27 UTC | if mut_type == 'raw', there will be no PPI network formatting/application | 27 May 2019, 14:33:27 UTC |
| 01397b6 | 0m1n0 | 27 May 2019, 14:32:06 UTC | Quantile normalisation modified using pandas.DataFrame.rank: if found two scores are same then assign the minimum rank to both the score | 27 May 2019, 14:32:06 UTC |
| ba37f72 | 0m1n0 | 01 April 2019, 11:44:31 UTC | Merge pull request #38 from 0m1n0/master some major arrangements and statistical representation | 01 April 2019, 11:44:31 UTC |
| 9cd4d46 | 0m1n0 | 01 April 2019, 11:32:09 UTC | more readability | 01 April 2019, 11:32:09 UTC |
| 00a44f5 | 0m1n0 | 01 April 2019, 11:30:49 UTC | reproducibility code uploaded | 01 April 2019, 11:30:49 UTC |
| 6403d6f | 0m1n0 | 28 February 2019, 11:35:18 UTC | STRING PPI file name changed: version added (v9) | 28 February 2019, 11:35:18 UTC |
| 987c3e9 | 0m1n0 | 08 January 2019, 15:40:35 UTC | incorrect individual indexing has been corrected: from phenotype individual indexes to mutation profile individual indexes | 08 January 2019, 15:40:35 UTC |
| a716d84 | 0m1n0 | 18 December 2018, 10:14:22 UTC | Load gene filtered data | 18 December 2018, 10:14:22 UTC |
| 5c278e4 | 0m1n0 | 18 December 2018, 10:13:49 UTC | few minor modifications | 18 December 2018, 10:13:49 UTC |
| d570e6c | 0m1n0 | 18 December 2018, 10:12:39 UTC | when bootstrap step is split, all sub-bootstrap files will be removed after merging | 18 December 2018, 10:12:39 UTC |
| 4585701 | 0m1n0 | 18 December 2018, 10:08:45 UTC | k=20->50: plot size adapted | 18 December 2018, 10:08:45 UTC |
| 3b77492 | 0m1n0 | 18 December 2018, 09:43:33 UTC | Go enrichment analysis: GO Slim. Save also significant p-value counts. | 18 December 2018, 09:43:33 UTC |
| 317d2da | 0m1n0 | 17 December 2018, 16:56:41 UTC | Get NaN when divided by zero | 17 December 2018, 16:56:41 UTC |
| 221d70a | 0m1n0 | 23 October 2018, 09:52:17 UTC | Mutation type (raw, diff, qn_mean, qn_median) is now directly done by parameter "mut_type" /// Parameter "qn" is removed /// Parameter "alpha" no longer needs the value "0" | 23 October 2018, 09:52:17 UTC |
| 591ef62 | 0m1n0 | 23 October 2018, 09:40:38 UTC | individual biostatistics test plot | 23 October 2018, 09:40:38 UTC |
| 0bdf576 | 0m1n0 | 23 October 2018, 09:38:52 UTC | GO enrichment test on gene clusters using Go Enrich | 23 October 2018, 09:38:52 UTC |
| c13457a | 0m1n0 | 23 October 2018, 09:37:52 UTC | - SRS and Vineland added in biostatistics test between individual clusters. - All biostatistics results will be saved in pickle file | 23 October 2018, 09:37:52 UTC |
| 906b85b | 0m1n0 | 01 October 2018, 13:11:24 UTC | sys.setrecursionlimit(10000) added in order to avoid recursion error during hierarchical clustering | 01 October 2018, 13:11:24 UTC |
| be4cc13 | 0m1n0 | 01 October 2018, 13:10:40 UTC | some print functions removed | 01 October 2018, 13:10:40 UTC |
| 281fce0 | 0m1n0 | 24 September 2018, 16:45:35 UTC | Calls functions have been updated | 24 September 2018, 16:45:35 UTC |
| 86b2a1a | 0m1n0 | 24 September 2018, 16:44:28 UTC | some print functions modified | 24 September 2018, 16:44:28 UTC |
| ab1414f | 0m1n0 | 24 September 2018, 16:43:24 UTC | hierarchical_clustering filename simplified | 24 September 2018, 16:43:24 UTC |
| a702c75 | 0m1n0 | 24 September 2018, 16:42:51 UTC | PPI_final filename simplified | 24 September 2018, 16:42:51 UTC |
| 6b9fa6f | 0m1n0 | 24 September 2018, 16:41:40 UTC | PPI data formatting by jupyter notebook added | 24 September 2018, 16:41:40 UTC |
| 24a6ffa | 0m1n0 | 12 September 2018, 13:39:02 UTC | nbs.py for run sub-bootstrap on Cluster using Slurm | 12 September 2018, 13:39:02 UTC |
| 8b52521 | 0m1n0 | 12 September 2018, 13:38:11 UTC | hierarchical_clustering and biostatistics parts are separated into 2 files | 12 September 2018, 13:38:11 UTC |
| bc725e9 | 0m1n0 | 12 September 2018, 13:37:16 UTC | clustering.py divided into nmf_bootstrap.py consensus_clustering.py | 12 September 2018, 13:37:16 UTC |
| 795615b | 0m1n0 | 12 September 2018, 13:35:52 UTC | all formatting functions merged | 12 September 2018, 13:35:52 UTC |
| 273975d | 0m1n0 | 11 September 2018, 12:36:52 UTC | new option added: NMF bootstrap could be dived into sub-bootstrap steps | 11 September 2018, 12:36:52 UTC |
| 9782abe | 0m1n0 | 11 September 2018, 12:34:26 UTC | all filtering functions merged into one general function | 11 September 2018, 12:34:26 UTC |
| bf5c8b7 | 0m1n0 | 11 September 2018, 12:32:25 UTC | save PPI file after patient filtering | 11 September 2018, 12:32:25 UTC |
| ab9e4f0 | 0m1n0 | 08 September 2018, 14:18:05 UTC | Formatting of raw STRING PPI data | 08 September 2018, 14:18:05 UTC |
| 0182bba | 0m1n0 | 05 September 2018, 13:42:05 UTC | parameter setting file created | 05 September 2018, 13:42:05 UTC |
| d616a16 | 0m1n0 | 22 August 2018, 09:25:02 UTC | Small individual cluster plot added | 22 August 2018, 09:25:02 UTC |
| f583800 | 0m1n0 | 22 August 2018, 08:59:50 UTC | Calculate individual & GENE distance from consensus clustering file. Get Entrez Gene ID of each clusters into output text file | 22 August 2018, 08:59:50 UTC |
| ded7eb1 | 0m1n0 | 03 August 2018, 13:50:59 UTC | adjacency matrix to binary values (0/1) | 03 August 2018, 13:50:59 UTC |
| 922ed61 | 0m1n0 | 01 August 2018, 15:08:33 UTC | load last version of STRING PPI dataset | 01 August 2018, 15:08:33 UTC |
| 82fb68a | 0m1n0 | 25 July 2018, 08:58:59 UTC | print bootstrap and distance matrix time. hierarchical_clustering_file search error fixed | 25 July 2018, 08:58:59 UTC |
| ae0b98e | 0m1n0 | 24 July 2018, 12:48:13 UTC | Merge pull request #37 from 0m1n0/master Biological statistics analysis from clusters | 24 July 2018, 12:48:13 UTC |
| bd02243 | 0m1n0 | 24 July 2018, 12:45:42 UTC | Reproducibility paper link uploaded | 24 July 2018, 12:45:42 UTC |
| aefedbc | 0m1n0 | 20 July 2018, 09:13:17 UTC | import some statistical test functions from scipy.stats | 20 July 2018, 09:13:17 UTC |
| e81a000 | 0m1n0 | 19 July 2018, 14:08:08 UTC | minimum/maximum mutation numbers included (before: excluded) | 19 July 2018, 14:08:08 UTC |
| c4daaeb | 0m1n0 | 19 July 2018, 13:59:50 UTC | addition of biological statistics analysis from clusters | 19 July 2018, 13:59:50 UTC |
| 89aa3c1 | 0m1n0 | 10 July 2018, 13:59:23 UTC | Merge pull request #36 from 0m1n0/master Distinction between several PPI data: Hofree's STRING (2013), latest STRING, APID and Y2H | 10 July 2018, 13:59:23 UTC |
| 45c91c8 | 0m1n0 | 10 July 2018, 13:55:18 UTC | Update README.md | 10 July 2018, 13:55:18 UTC |
| 5fc8182 | 0m1n0 | 10 July 2018, 13:53:46 UTC | Update README.md | 10 July 2018, 13:53:46 UTC |
| 6ceab8d | 0m1n0 | 27 June 2018, 15:24:59 UTC | ppi_data of STRING changed: from 'STRING' to 'Hofree_STRING' | 27 June 2018, 15:24:59 UTC |
| 8a5175c | 0m1n0 | 27 June 2018, 15:16:36 UTC | psi network loading function name changed | 27 June 2018, 15:16:36 UTC |
| 280e06e | 0m1n0 | 27 June 2018, 14:32:27 UTC | save ppi matrix in .mat format | 27 June 2018, 14:32:27 UTC |
| 5cec999 | Guillaume Dumas | 06 June 2018, 11:25:59 UTC | Merge pull request #35 from 0m1n0/master simulation, PAC, APID, SSC, filtering | 06 June 2018, 11:25:59 UTC |
| 0a9104f | 0m1n0 | 06 June 2018, 11:15:45 UTC | best neighbours filtering error resolved | 06 June 2018, 11:15:45 UTC |
| 3fcabcf | 0m1n0 | 05 June 2018, 14:50:25 UTC | simulation network plot vmax value changed | 05 June 2018, 14:50:25 UTC |
| d58ff2d | 0m1n0 | 25 May 2018, 09:32:06 UTC | statistics test output file: print p-values if <= 0.05 | 25 May 2018, 09:32:06 UTC |
| 485a7fb | 0m1n0 | 25 May 2018, 09:30:07 UTC | results directories and files names changed | 25 May 2018, 09:30:07 UTC |
| 40f413b | 0m1n0 | 22 May 2018, 13:45:59 UTC | small similarity matrix figure and statistic test results will be saved in folders "figure/" and "text/" | 22 May 2018, 13:45:59 UTC |
| dca835f | 0m1n0 | 22 May 2018, 13:44:46 UTC | distinction between overall_mutation_profile and specific_mutation_profile depending on gene_data: all, brain1SD, brain2SD, pli, sfari | 22 May 2018, 13:44:46 UTC |
| bc76fd4 | 0m1n0 | 27 April 2018, 17:16:32 UTC | SSC result analysis added: statistical test and barplot | 27 April 2018, 17:16:32 UTC |
| 71fba6b | 0m1n0 | 24 April 2018, 15:59:15 UTC | choice to compute gene clustering added: new parameter "compute_gene_clustering" -> True/False | 24 April 2018, 15:59:15 UTC |
| c91f505 | 0m1n0 | 24 April 2018, 08:36:42 UTC | Addition of load SSC (SSC1 and SSC2) data functions; Addition of new parameters, ssc_type and ssc_subgroups | 24 April 2018, 08:36:42 UTC |
| a0a2b6d | 0m1n0 | 19 April 2018, 14:34:02 UTC | SSC mutation profile formatting new parameter added: 'ssc_type': 'LoF', 'missense' | 19 April 2018, 14:34:02 UTC |
| 17eaa0e | 0m1n0 | 19 April 2018, 14:09:24 UTC | Load APID PPI adjacency matrix if no exist, calculate adjacency matrix | 19 April 2018, 14:09:24 UTC |
| 853a532 | 0m1n0 | 06 April 2018, 15:28:19 UTC | Merge branch 'simulation' * simulation: new version of APID data APID dataset ID mapping UniProt -> Entrez Gene Selection of one unique EntrzGene ID: on going... load data, ID mapping and filtering Simulation suitable for the numbers of patients and pathways (sub-networks) Clustering performance calculated by PAC score using R package confusion matrix fonctions for simulation added some file names changed fixed node positions of PPI reloaded stratipy with small random PPI and small simulated mutation profile | 06 April 2018, 15:28:19 UTC |
| 43098a4 | 0m1n0 | 06 April 2018, 15:14:16 UTC | new version of APID data | 06 April 2018, 15:14:16 UTC |
| e996a08 | 0m1n0 | 08 March 2018, 15:27:14 UTC | APID dataset ID mapping UniProt -> Entrez Gene | 08 March 2018, 15:27:14 UTC |
| f4ec827 | 0m1n0 | 09 February 2018, 17:28:33 UTC | Selection of one unique EntrzGene ID: on going... | 09 February 2018, 17:28:33 UTC |
| ab1f329 | 0m1n0 | 09 February 2018, 17:27:15 UTC | load data, ID mapping and filtering | 09 February 2018, 17:27:15 UTC |
| fa93866 | 0m1n0 | 05 February 2018, 14:50:23 UTC | Simulation suitable for the numbers of patients and pathways (sub-networks) | 05 February 2018, 14:50:23 UTC |
| 3aa05d9 | 0m1n0 | 29 January 2018, 16:24:34 UTC | Clustering performance calculated by PAC score using R package | 29 January 2018, 16:24:34 UTC |
| 858d44e | 0m1n0 | 17 January 2018, 13:23:44 UTC | confusion matrix fonctions for simulation added | 17 January 2018, 13:23:44 UTC |
| 4804906 | 0m1n0 | 15 January 2018, 09:08:13 UTC | some file names changed | 15 January 2018, 09:08:13 UTC |
| 97ca525 | 0m1n0 | 05 December 2017, 16:49:05 UTC | fixed node positions of PPI reloaded | 05 December 2017, 16:49:05 UTC |
| a1e21de | 0m1n0 | 05 December 2017, 12:33:22 UTC | stratipy with small random PPI and small simulated mutation profile | 05 December 2017, 12:33:22 UTC |
| 24fcbe9 | 0m1n0 | 05 December 2017, 12:29:24 UTC | some unit tests on filtering_diffusion.py | 05 December 2017, 12:29:24 UTC |
| 8d626f3 | Guillaume Dumas | 05 December 2017, 10:34:19 UTC | Merge pull request #34 from deep-introspection/master Packaging for pip | 05 December 2017, 10:34:19 UTC |
| 22be396 | deep-introspection | 05 December 2017, 10:33:40 UTC | Packaging for pip | 05 December 2017, 10:33:40 UTC |
| 68a2916 | 0m1n0 | 06 November 2017, 16:28:09 UTC | Zenodo logo changed | 06 November 2017, 16:28:09 UTC |
| 33f65fe | 0m1n0 | 06 November 2017, 16:27:13 UTC | Zenodo logo changed | 06 November 2017, 16:27:13 UTC |
| 91d319d | 0m1n0 | 06 November 2017, 16:25:59 UTC | Zenodo logo color changed | 06 November 2017, 16:25:59 UTC |
| 5236cca | 0m1n0 | 06 November 2017, 15:21:49 UTC | Add Zenodo URL | 06 November 2017, 15:21:49 UTC |
