0000000000000000000000000000000000000000 5e8a572d562a7eecfeb7755cee94469e6ead1313 richelbilderbeek <richel@richelbilderbeek.nl> 1633517444 +0200	branch: Created from refs/remotes/origin/develop
5e8a572d562a7eecfeb7755cee94469e6ead1313 686e3219542bd85d7e71831575e2c03defdfa454 richelbilderbeek <richel@richelbilderbeek.nl> 1633517447 +0200	merge master: Fast-forward
686e3219542bd85d7e71831575e2c03defdfa454 2ef1bf55c99a6a49861a81d4dbe415dd59e206e8 richelbilderbeek <richel@richelbilderbeek.nl> 1633517523 +0200	commit: Install 'richelbilderbeek/bianchi_et_al_2017'
2ef1bf55c99a6a49861a81d4dbe415dd59e206e8 b3b2aaa88d51b6b1100a47d48112d29433287900 richelbilderbeek <richel@richelbilderbeek.nl> 1633517733 +0200	commit: Download Schellens et al. XLSL sheet
b3b2aaa88d51b6b1100a47d48112d29433287900 c998ec252fb22ddc8ce25eb2eceef2e8733301c4 richelbilderbeek <richel@richelbilderbeek.nl> 1633519629 +0200	commit: Fix Makefile
c998ec252fb22ddc8ce25eb2eceef2e8733301c4 3656f469ce00ca917d9411c4ae11685982d22095 richelbilderbeek <richel@richelbilderbeek.nl> 1633519720 +0200	commit: Fix Makefile
3656f469ce00ca917d9411c4ae11685982d22095 45c418bb0f8680822f9ebc45b1cf410a19ee0ee4 richelbilderbeek <richel@richelbilderbeek.nl> 1633522653 +0200	commit: Install deps in Makefile
45c418bb0f8680822f9ebc45b1cf410a19ee0ee4 776092837572655bd5b995dc0c7c1287a3faba74 richelbilderbeek <richel@richelbilderbeek.nl> 1633526383 +0200	commit: Show build badges
776092837572655bd5b995dc0c7c1287a3faba74 cf60ba43dcb97f434dc78825584ee14eabc62c35 richelbilderbeek <richel@richelbilderbeek.nl> 1633526466 +0200	commit: GHA logo
cf60ba43dcb97f434dc78825584ee14eabc62c35 32fd28e7a57aa44b8b8e0d6f093cb99fcce9196c richelbilderbeek <richel@richelbilderbeek.nl> 1633951248 +0200	commit: Add IEDB results, progress https://github.com/richelbilderbeek/bbbq_article/issues/229
32fd28e7a57aa44b8b8e0d6f093cb99fcce9196c a6ccafbef6131ea3452ec4205c3a7cb0e8a0a25c richelbilderbeek <richel@richelbilderbeek.nl> 1633951423 +0200	commit: No CSVs in 'iedb' folder
a6ccafbef6131ea3452ec4205c3a7cb0e8a0a25c e7b2f4ad3f278599cee5319561fe525e24e3df5c richelbilderbeek <richel@richelbilderbeek.nl> 1633960633 +0200	commit: EOD
e7b2f4ad3f278599cee5319561fe525e24e3df5c 151f3baac194a7b94487a909c042188d930c2985 richelbilderbeek <richel@richelbilderbeek.nl> 1634542972 +0200	commit: Show result
151f3baac194a7b94487a909c042188d930c2985 5544ab587f756e7b7664a59743e6b7c11dd90309 richelbilderbeek <richel@richelbilderbeek.nl> 1635322603 +0200	commit: Can create iedb.csv
5544ab587f756e7b7664a59743e6b7c11dd90309 ef8c155ad577729a1399ee2c1a15334b28151d23 richelbilderbeek <richel@richelbilderbeek.nl> 1635325894 +0200	commit: Add IEDB data, progress https://github.com/richelbilderbeek/bbbq_article/issues/229
ef8c155ad577729a1399ee2c1a15334b28151d23 9628b01345f07b0515eb5f5d5eb15ad9e8387090 richelbilderbeek <richel@richelbilderbeek.nl> 1635327557 +0200	commit: 'create_tmhs_pureseqtm_csv.R' and 'create_tmhs_tmhmm_csv.R' work on IEDB data
9628b01345f07b0515eb5f5d5eb15ad9e8387090 02618b638aac7583787fdb3bbbd24d2c49eeb9d6 richelbilderbeek <richel@richelbilderbeek.nl> 1635427423 +0200	commit: EOD
02618b638aac7583787fdb3bbbd24d2c49eeb9d6 b6af0ec1b3cd0ac176590fbce87b747e1f474eff richelbilderbeek <richel@richelbilderbeek.nl> 1635504086 +0200	commit: Can create results for IEDB studies, progress #229
b6af0ec1b3cd0ac176590fbce87b747e1f474eff 0e5daa9c5e3a9757849c6f7bfce324ecb1aae031 richelbilderbeek <richel@richelbilderbeek.nl> 1635859811 +0100	commit: Allow IEDB with B cells, MHC ligands and T cells
0e5daa9c5e3a9757849c6f7bfce324ecb1aae031 9ca89717d05f252feaa8b6b4e1b06ad27eb09d95 richelbilderbeek <richel@richelbilderbeek.nl> 1635862148 +0100	commit: Allow more datasets
9ca89717d05f252feaa8b6b4e1b06ad27eb09d95 933dff6938815c9feb92775ea44178c961a0aa06 richelbilderbeek <richel@richelbilderbeek.nl> 1635868625 +0100	commit: Allow to work with three types of IEDB data
933dff6938815c9feb92775ea44178c961a0aa06 77609d1d6e20990be8d2c189c59e1aa3e1b53397 richelbilderbeek <richel@richelbilderbeek.nl> 1635874742 +0100	commit: Fix scripts
77609d1d6e20990be8d2c189c59e1aa3e1b53397 4a2d08ef5e7d1340ed0668b942b1134fba186c40 richelbilderbeek <richel@richelbilderbeek.nl> 1635930867 +0100	commit: Do B and T cells
4a2d08ef5e7d1340ed0668b942b1134fba186c40 3f37552e8745257869c313e59f1612718a1343b0 richelbilderbeek <richel@richelbilderbeek.nl> 1635933821 +0100	commit: Allow B cell, T cells and MHC ligands
3f37552e8745257869c313e59f1612718a1343b0 3e9a555a0eebcb09fc91a729cd371ff9955ce920 richelbilderbeek <richel@richelbilderbeek.nl> 1635934380 +0100	commit: Can get to results
3e9a555a0eebcb09fc91a729cd371ff9955ce920 c001ba40c15963b6929836e4d0bc72d3aa8cb3fc richelbilderbeek <richel@richelbilderbeek.nl> 1635941442 +0100	commit: Add IEDB data, without MHC ligands
c001ba40c15963b6929836e4d0bc72d3aa8cb3fc e48c39b28c3e315a1a55359356e834ff1a11ed1b richelbilderbeek <richel@richelbilderbeek.nl> 1635945972 +0100	commit: Create figure 2d
e48c39b28c3e315a1a55359356e834ff1a11ed1b 22dfb0c7a2976adda2ff217d94ff6062ee3db7c2 richelbilderbeek <richel@richelbilderbeek.nl> 1635946296 +0100	commit: Add numbers
22dfb0c7a2976adda2ff217d94ff6062ee3db7c2 e3a3a9195d9dc2646ab1c3579812ca0c8429c452 richelbilderbeek <richel@richelbilderbeek.nl> 1636026346 +0100	commit: EOD
e3a3a9195d9dc2646ab1c3579812ca0c8429c452 6090487410c92e73583af5fb68ac10eeee4efebe richelbilderbeek <richel@richelbilderbeek.nl> 1636049045 +0100	commit: Can use MHC ligands
6090487410c92e73583af5fb68ac10eeee4efebe 7a204d3db914eb24e32fd5b766af9bdd94fc5212 richelbilderbeek <richel@richelbilderbeek.nl> 1636053349 +0100	commit: Can use MHC ligands for MHC alleles
7a204d3db914eb24e32fd5b766af9bdd94fc5212 20e2995bc34c36afdabc0b951514c1985521fdee richelbilderbeek <richel@richelbilderbeek.nl> 1636053405 +0100	commit: Use MHC ligands
20e2995bc34c36afdabc0b951514c1985521fdee 164c58e6bd3289b27effe1823b4e1cda776576e1 richelbilderbeek <richel@richelbilderbeek.nl> 1636053573 +0100	commit: Can use MHC ligands
164c58e6bd3289b27effe1823b4e1cda776576e1 2868f51fb5d826983fc8f488e200465d5749c7b7 richelbilderbeek <richel@richelbilderbeek.nl> 1636057472 +0100	commit: Can do all alleles
2868f51fb5d826983fc8f488e200465d5749c7b7 f3c56033c068129c73b6718cea1f8149f38de57b richelbilderbeek <richel@richelbilderbeek.nl> 1636091431 +0100	commit: Can work on a per-allele or all-allele base
f3c56033c068129c73b6718cea1f8149f38de57b 21bb5c957257076ff0f6bf6da1078fa0d92304d9 richelbilderbeek <richel@richelbilderbeek.nl> 1636120424 +0100	commit: Can get results for all or per alleles
21bb5c957257076ff0f6bf6da1078fa0d92304d9 d34756959fff16531fe7d52605a4e2a6116eed4c richelbilderbeek <richel@richelbilderbeek.nl> 1636133194 +0100	commit: EOD
d34756959fff16531fe7d52605a4e2a6116eed4c 96ba649da8739c1199572df880ce0d03ecf6e4d1 richelbilderbeek <richel@richelbilderbeek.nl> 1636402545 +0100	commit: Depend on iedbr
96ba649da8739c1199572df880ce0d03ecf6e4d1 70889f249a1364ff6ffb589af08487a350041427 richelbilderbeek <richel@richelbilderbeek.nl> 1636446924 +0100	commit: Work with iedbr
70889f249a1364ff6ffb589af08487a350041427 30c717fc06128dae2ecac2a22fcf5748e811e4a3 richelbilderbeek <richel@richelbilderbeek.nl> 1636447009 +0100	commit: Replace complex code by call to 'iedbr
30c717fc06128dae2ecac2a22fcf5748e811e4a3 3d913f54158295e03d916d39675b5c68f802e202 richelbilderbeek <richel@richelbilderbeek.nl> 1636447088 +0100	commit: 'bbbq' has clean MHC allele names
3d913f54158295e03d916d39675b5c68f802e202 4342cbdc6313f2891bcdd9ab1b9b37736e47c311 richelbilderbeek <richel@richelbilderbeek.nl> 1636447315 +0100	commit: Using 'iedbr'
4342cbdc6313f2891bcdd9ab1b9b37736e47c311 f01b5bf29ea175c3349862408f3fb9010ca21945 richelbilderbeek <richel@richelbilderbeek.nl> 1636453329 +0100	commit: Can limit to any number of queries
f01b5bf29ea175c3349862408f3fb9010ca21945 fbdae00acfc929c73cc689dd42d5e69785cfa609 richelbilderbeek <richel@richelbilderbeek.nl> 1636453510 +0100	commit: Can query IEDB properly
fbdae00acfc929c73cc689dd42d5e69785cfa609 a064f621eadd1daee632552d9df4b34efe74a37d richelbilderbeek <richel@richelbilderbeek.nl> 1636454574 +0100	commit: Stick to 'max_n_queries' maximum amount of queries
a064f621eadd1daee632552d9df4b34efe74a37d 47fae85ec41e6832526f9f9f848d2a5a92f575a0 richelbilderbeek <richel@richelbilderbeek.nl> 1636460831 +0100	commit: Collect MHC ligands and epitopes side by side
47fae85ec41e6832526f9f9f848d2a5a92f575a0 2986f35f18fcd5fce2cec1c3c07b9b5b5f76cf3d richelbilderbeek <richel@richelbilderbeek.nl> 1636460937 +0100	commit: Can 'make iedb_mhc_ligand_and_allele.csv'
2986f35f18fcd5fce2cec1c3c07b9b5b5f76cf3d 8d3cb1142ede7745e1430a671fd5415e8e8760b8 richelbilderbeek <richel@richelbilderbeek.nl> 1636463662 +0100	commit: First collect general epitope tables
8d3cb1142ede7745e1430a671fd5415e8e8760b8 cf9880c55f2e791c46a8b74c2d6c77a93a50e999 richelbilderbeek <richel@richelbilderbeek.nl> 1636467352 +0100	commit: Use IEDB tables that exist
cf9880c55f2e791c46a8b74c2d6c77a93a50e999 c38f438f58b913fda4bdf86f3558a5c0db987132 richelbilderbeek <richel@richelbilderbeek.nl> 1636467397 +0100	commit: Fix typo
c38f438f58b913fda4bdf86f3558a5c0db987132 de698e80bc946b2b5d35bb180e47c6ebc8830f11 richelbilderbeek <richel@richelbilderbeek.nl> 1636467483 +0100	commit: Fix typo
de698e80bc946b2b5d35bb180e47c6ebc8830f11 38f56296c0faf14e6127c2347902dd9920ef52c3 richelbilderbeek <richel@richelbilderbeek.nl> 1636468277 +0100	commit: Can get all epitopes on a per-allele-name basis
38f56296c0faf14e6127c2347902dd9920ef52c3 7d7a199b31485b5a6aa7ae8f3aadbd2de09a4b36 richelbilderbeek <richel@richelbilderbeek.nl> 1636468984 +0100	commit: Use clean allele names
7d7a199b31485b5a6aa7ae8f3aadbd2de09a4b36 5d5204a5effef0e3dc0b67d74a277e8edb113453 richelbilderbeek <richel@richelbilderbeek.nl> 1636470681 +0100	commit: Can do more
5d5204a5effef0e3dc0b67d74a277e8edb113453 a51d618a72b40292c8c66cd188d4384b022a4b22 richelbilderbeek <richel@richelbilderbeek.nl> 1636471257 +0100	commit: Use 'allele_name' instead of the misnomer 'haplotype'
a51d618a72b40292c8c66cd188d4384b022a4b22 36dee531a2b4c43c72cdb3c071c9401f6a10f0b6 richelbilderbeek <richel@richelbilderbeek.nl> 1636471280 +0100	commit: Add namespace
36dee531a2b4c43c72cdb3c071c9401f6a10f0b6 5bffcd915a96176a7079f3f58b6d93cab5cb8480 richelbilderbeek <richel@richelbilderbeek.nl> 1636487279 +0100	commit: Improve 'create_results_csv.R'
5bffcd915a96176a7079f3f58b6d93cab5cb8480 ddaee56b6ec3f05ebe1cfc93d493350c9e43e344 richelbilderbeek <richel@richelbilderbeek.nl> 1636492083 +0100	commit: Also save allele name
ddaee56b6ec3f05ebe1cfc93d493350c9e43e344 6dacf48e9141eb94dfbc409ffd35988dbb8f1a6b richelbilderbeek <richel@richelbilderbeek.nl> 1636497781 +0100	commit: Create results_per_allele_per_allele.csv
6dacf48e9141eb94dfbc409ffd35988dbb8f1a6b 88a08759674e194c5a23c8eb72765d17070a663b richelbilderbeek <richel@richelbilderbeek.nl> 1636497971 +0100	commit: Fix typo
88a08759674e194c5a23c8eb72765d17070a663b 5890adeb1e3e0865108d40acb3fc164c7805f315 richelbilderbeek <richel@richelbilderbeek.nl> 1636502563 +0100	commit: Can create figure 2c and 2d
5890adeb1e3e0865108d40acb3fc164c7805f315 a5ef651d73336835aee96ada1c75de32b9f19dfe richelbilderbeek <richel@richelbilderbeek.nl> 1636505725 +0100	commit: Create figure 2a
a5ef651d73336835aee96ada1c75de32b9f19dfe 3dd9119c13ffbaef6e7115b0e70bc300a2f2b6af richelbilderbeek <richel@richelbilderbeek.nl> 1636506594 +0100	commit: Can create fig 2b
3dd9119c13ffbaef6e7115b0e70bc300a2f2b6af 40ad823458f9b5e7e02aa6c34d7b03fb3f58c7ff richelbilderbeek <richel@richelbilderbeek.nl> 1636819343 +0100	commit: Swapped 2b and 2c files
40ad823458f9b5e7e02aa6c34d7b03fb3f58c7ff 3bc14a9042dab70c800fecc42ac1f21afb2cfe80 richelbilderbeek <richel@richelbilderbeek.nl> 1636819383 +0100	commit: Swapped 2b and 2c files
3bc14a9042dab70c800fecc42ac1f21afb2cfe80 4f6bb8ec02e3943692eb2be8740ea7493f8ae16b richelbilderbeek <richel@richelbilderbeek.nl> 1636819522 +0100	commit: No Bergseng and Schellens
4f6bb8ec02e3943692eb2be8740ea7493f8ae16b 49ae19c12bced8190156f0bed6fe052638b0ef90 richelbilderbeek <richel@richelbilderbeek.nl> 1636819590 +0100	commit: Simplify
49ae19c12bced8190156f0bed6fe052638b0ef90 48f091892a3583a2eb64b93e19d53b0e532f06dd richelbilderbeek <richel@richelbilderbeek.nl> 1636819691 +0100	commit: Fix name
48f091892a3583a2eb64b93e19d53b0e532f06dd be51a98c118fd07a04f07f9eaec1585acc7712be richelbilderbeek <richel@richelbilderbeek.nl> 1636819814 +0100	commit: Fix script
be51a98c118fd07a04f07f9eaec1585acc7712be 99825527f4d19ec0766da5554f47c5ac09bcf077 richelbilderbeek <richel@richelbilderbeek.nl> 1636820195 +0100	commit: Renamed
99825527f4d19ec0766da5554f47c5ac09bcf077 5ae8eb8d4ac55dcdaeeaec474dfb67fc00adc9cd richelbilderbeek <richel@richelbilderbeek.nl> 1636825525 +0100	commit: EOD
5ae8eb8d4ac55dcdaeeaec474dfb67fc00adc9cd 684c25ea0755c24e987371e1075d61fa3ae2dc83 richelbilderbeek <richel@richelbilderbeek.nl> 1636829374 +0100	commit: Fix calculation
684c25ea0755c24e987371e1075d61fa3ae2dc83 e8c97940183b8e28df9a2375f453d7f81397eae9 richelbilderbeek <richel@richelbilderbeek.nl> 1636914801 +0100	commit: Can create tex
e8c97940183b8e28df9a2375f453d7f81397eae9 5e3b7b3899d9a84632c68b6d15f2b766ce7765c1 richelbilderbeek <richel@richelbilderbeek.nl> 1637233772 +0100	commit: Add confidence intervals for figure2a.png
5e3b7b3899d9a84632c68b6d15f2b766ce7765c1 9514f4e52586ae3ba328bd12026bbc65c4f595fb richelbilderbeek <richel@richelbilderbeek.nl> 1637233784 +0100	commit: Add confidence intervals for figure2a.png
9514f4e52586ae3ba328bd12026bbc65c4f595fb e744efd3c07f95f24d6b98f9018bbf5f9b7c16c2 richelbilderbeek <richel@richelbilderbeek.nl> 1637235950 +0100	commit: Figure 2b has coincidence interval
e744efd3c07f95f24d6b98f9018bbf5f9b7c16c2 7756fe8446f660f74f004d2390027a87ab354bf8 richelbilderbeek <richel@richelbilderbeek.nl> 1637235977 +0100	commit: Figure 2b has coincidence interval
7756fe8446f660f74f004d2390027a87ab354bf8 482dfb63385d2752bad7c9c0cefb5152a48129d6 richelbilderbeek <richel@richelbilderbeek.nl> 1637236670 +0100	commit: Indeed, '(' is a round bracket, not a round brace, thanks Geert
