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• 24d7820165
  
  Replace niv with flakes master 0.2.2 coolneng 2021-11-02 16:11:17 +01:00
• 3d8e0fe114
  
  Bump nixpkgs revision 0.2.1 coolneng 2021-07-06 17:26:52 +02:00
• 2058fc96d7
  
  Consider the read start in the Cys location 0.2.0 coolneng 2021-05-15 17:49:39 +02:00
• e4189cab01
  
  Choose the normal phenotype sequence for TRBJ2-2 coolneng 2021-05-15 17:36:58 +02:00
• 2acec89f84
  
  Rename output file to curesim-HVR.fastq coolneng 2021-05-14 20:01:56 +02:00
• 91b3e37bd8
  
  Start j_alignment with the portion after the Cys coolneng 2021-05-13 19:06:58 +02:00
• bf33b65191
  
  Convert org mode README to markdown coolneng 2021-05-05 12:23:23 +02:00
• e8f03189c2
  
  Document the alignment script 0.1.1 coolneng 2021-05-04 19:25:11 +02:00
• f4b7a41599
  
  Document the repertoire script coolneng 2021-05-04 18:34:15 +02:00
• 9e8beefd38
  
  Remove redundant directories coolneng 2021-05-04 11:12:47 +02:00
• 40205706e1
  
  Bump nixpkgs revision coolneng 2021-05-04 02:28:12 +02:00
• 8ffa86a965
  
  Elaborate on the project description in the README coolneng 2021-05-04 02:01:10 +02:00
• 1f7b40d224
  
  Remove redundant JDK dependency coolneng 2021-05-04 01:48:45 +02:00
• ad8abcc4fc
  
  Add usage instructions to the README 0.1.0 coolneng 2021-05-04 01:28:49 +02:00
• 6440816a87
  
  Remove imperative installation instructions coolneng 2021-05-04 00:59:05 +02:00
• 0e005735bc
  
  Create a Nix derivation for CuReSim coolneng 2021-05-04 00:57:35 +02:00
• 4f0936718b
  
  Add installation instruction to README coolneng 2021-05-03 23:27:19 +02:00
• 1b6e2d13ea
  
  Remove development dependencies coolneng 2021-05-03 23:22:16 +02:00
• 36eb73b458
  
  Add alignment to generation script coolneng 2021-05-03 21:51:48 +02:00
• 81a57657fe
  
  Fix HVR end position computation coolneng 2021-05-03 21:51:32 +02:00
• 5afe040592
  
  Isolate HVR sequence and save it to a file coolneng 2021-05-03 21:15:40 +02:00
• c250c139dd
  
  Implement cysteine location in v_alignment coolneng 2021-04-27 19:34:01 +02:00
• 4dec2061fc
  
  Generate FASTQ files from the simulated repertoire coolneng 2021-04-22 13:36:43 +02:00
• 4adb92e901
  
  Export original CDR3 to a file coolneng 2021-04-22 11:54:40 +02:00
• 83819b296b
  
  Save vj_sequences in a dataframe coolneng 2021-04-22 01:18:25 +02:00
• a7c1df5ce2
  
  Refactor get_vj_sequence function coolneng 2021-04-22 01:17:35 +02:00
• 81ebd4fbbe
  
  Rename function arguments to improve readability coolneng 2021-04-21 22:12:29 +02:00
• 659f0097d8
  
  Get V and J sequences from sequence ID coolneng 2021-04-21 21:29:03 +02:00
• fb5d781c66
  
  Add space to sequence ID for easier parsing coolneng 2021-04-21 21:02:56 +02:00
• 35406497a3
  
  Format generation script coolneng 2021-04-21 20:11:56 +02:00
• b771071974
  
  Remove csv from gitignore coolneng 2021-04-21 20:11:32 +02:00
• 2a997a3e5c
  
  Rename sequencing_runs to number_of_reads coolneng 2021-04-21 20:09:02 +02:00
• 1020d610d3
  
  Run CuReSim n times for each sequence coolneng 2021-04-21 20:00:13 +02:00
• 5154a35fca
  
  Remove sequencing runs argument from repertoire coolneng 2021-04-21 19:59:38 +02:00
• 18ffbf9a75
  
  Add v_call and j_call to sequence ID coolneng 2021-04-21 18:46:00 +02:00
• 82fdfdc6b9
  
  Exchange pattern and subject in the alignment coolneng 2021-04-08 18:31:50 +02:00
• dd9f7ffde4
  
  Remove redundant HVR sequence construction coolneng 2021-04-07 19:49:44 +02:00
• e694ee3292
  
  Select the first sequence matching the identifier coolneng 2021-04-07 18:41:14 +02:00
• e5a7b726a9
  
  Add v_segments and j_segments objects coolneng 2021-04-07 18:32:58 +02:00
• 38b35f7d12
  
  Align full sequences efficiently coolneng 2021-04-07 18:31:39 +02:00
• f81e4af94e
  
  Amplify VDJ sequences to simplify parsing coolneng 2021-03-29 22:57:36 +02:00
• 576597cb04
  
  Remove redundant sequencing runs argument coolneng 2021-03-29 20:30:16 +02:00
• 13f453718d
  
  Implement HVR sequence alignment coolneng 2021-03-27 09:36:59 +01:00
• 3a10380d8c
  
  Construct a dataframe containing the HVR region coolneng 2021-03-25 21:53:49 +01:00
• 8f5b9ee698
  
  Parse curesim and VDJ sequences from files coolneng 2021-03-23 20:54:31 +01:00
• 66b39485a9
  
  Save vdj alignment sequences to a CSV coolneng 2021-03-23 19:33:32 +01:00
• 97b8914cd5
  
  Add literate programming notebook coolneng 2021-03-23 18:24:01 +01:00
• bc666a37c7
  
  Delete CuReSim log file after execution coolneng 2021-03-11 21:28:58 +01:00
• d5bf8f3b72
  
  Remove redundant casting coolneng 2021-03-11 21:28:00 +01:00
• 762791829a
  
  Save v_call and j_call to a text file coolneng 2021-03-11 21:03:16 +01:00
• 7b15df7614
  
  Simplify repertoire generation coolneng 2021-03-10 12:34:20 +01:00
• f4a001f821
  
  Change CuReSim output file extension to FASTQ coolneng 2021-03-10 12:33:25 +01:00
• d2e45bc00f
  
  Change output format to FASTA coolneng 2021-03-02 20:08:14 +01:00
• deb1066982
  
  Set CuReSim read size to 350 bases coolneng 2021-03-02 20:07:05 +01:00
• edc4a72425
  
  Update gitignore coolneng 2021-02-28 02:24:23 +01:00
• 42aadb1e28
  
  Add sequencing runs CLI argument coolneng 2021-02-28 02:23:58 +01:00
• ae5014fd74
  
  Remove a_chain generation coolneng 2021-02-28 02:23:28 +01:00
• 34722f3ebf
  
  Add gitignore coolneng 2021-02-26 03:11:34 +01:00
• b51706d0c0
  
  Create a script that executes the pipeline coolneng 2021-02-26 02:59:22 +01:00
• 53dda36c66
  
  Export the data to FASTQ files coolneng 2021-02-26 02:20:11 +01:00
• b035c496f7
  
  Filter the relevant columns from immuneSIM output coolneng 2021-02-26 02:19:40 +01:00
• 2cece5e53e
  
  Set number of sequences via a CLI argument coolneng 2021-02-25 20:02:11 +01:00
• 010849d4c9
  
  Generate both alfa and beta chains coolneng 2021-02-25 20:00:35 +01:00
• f63fabac4f
  
  Add development tools as project dependencies coolneng 2021-02-22 21:40:01 +01:00
• 5c37fad320
  
  Add data directories coolneng 2021-02-22 00:59:32 +01:00
• 6cb20a7b1e
  
  Create a repertoire simulation prototype coolneng 2021-02-21 20:59:39 +01:00
• 04936c47cc
  
  Initial commit coolneng 2021-02-17 23:33:54 +01:00