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67 Commits

Author SHA1 Message Date
coolneng 24d7820165
Replace niv with flakes 2021-11-02 16:11:17 +01:00
coolneng 3d8e0fe114
Bump nixpkgs revision 2021-07-06 17:26:52 +02:00
coolneng 2058fc96d7
Consider the read start in the Cys location 2021-05-15 17:49:39 +02:00
coolneng e4189cab01
Choose the normal phenotype sequence for TRBJ2-2 2021-05-15 17:36:58 +02:00
coolneng 2acec89f84
Rename output file to curesim-HVR.fastq 2021-05-14 20:01:56 +02:00
coolneng 91b3e37bd8
Start j_alignment with the portion after the Cys 2021-05-13 19:06:58 +02:00
coolneng bf33b65191
Convert org mode README to markdown 2021-05-05 12:39:07 +02:00
coolneng e8f03189c2
Document the alignment script 2021-05-04 19:25:11 +02:00
coolneng f4b7a41599
Document the repertoire script 2021-05-04 18:34:28 +02:00
coolneng 9e8beefd38
Remove redundant directories 2021-05-04 11:13:25 +02:00
coolneng 40205706e1
Bump nixpkgs revision 2021-05-04 02:28:12 +02:00
coolneng 8ffa86a965
Elaborate on the project description in the README 2021-05-04 02:01:10 +02:00
coolneng 1f7b40d224
Remove redundant JDK dependency 2021-05-04 01:57:34 +02:00
coolneng ad8abcc4fc
Add usage instructions to the README 2021-05-04 01:28:49 +02:00
coolneng 6440816a87
Remove imperative installation instructions 2021-05-04 00:59:05 +02:00
coolneng 0e005735bc
Create a Nix derivation for CuReSim 2021-05-04 00:57:35 +02:00
coolneng 4f0936718b
Add installation instruction to README 2021-05-03 23:27:19 +02:00
coolneng 1b6e2d13ea
Remove development dependencies 2021-05-03 23:22:16 +02:00
coolneng 36eb73b458
Add alignment to generation script 2021-05-03 21:51:48 +02:00
coolneng 81a57657fe
Fix HVR end position computation 2021-05-03 21:51:32 +02:00
coolneng 5afe040592
Isolate HVR sequence and save it to a file 2021-05-03 21:15:40 +02:00
coolneng c250c139dd
Implement cysteine location in v_alignment 2021-04-27 19:34:01 +02:00
coolneng 4dec2061fc
Generate FASTQ files from the simulated repertoire 2021-04-22 13:59:45 +02:00
coolneng 4adb92e901
Export original CDR3 to a file 2021-04-22 11:54:58 +02:00
coolneng 83819b296b
Save vj_sequences in a dataframe 2021-04-22 01:18:25 +02:00
coolneng a7c1df5ce2
Refactor get_vj_sequence function 2021-04-22 01:17:35 +02:00
coolneng 81ebd4fbbe
Rename function arguments to improve readability 2021-04-21 22:12:29 +02:00
coolneng 659f0097d8
Get V and J sequences from sequence ID 2021-04-21 21:29:03 +02:00
coolneng fb5d781c66
Add space to sequence ID for easier parsing 2021-04-21 21:02:56 +02:00
coolneng 35406497a3
Format generation script 2021-04-21 20:11:56 +02:00
coolneng b771071974
Remove csv from gitignore 2021-04-21 20:11:32 +02:00
coolneng 2a997a3e5c
Rename sequencing_runs to number_of_reads 2021-04-21 20:09:02 +02:00
coolneng 1020d610d3
Run CuReSim n times for each sequence 2021-04-21 20:00:13 +02:00
coolneng 5154a35fca
Remove sequencing runs argument from repertoire 2021-04-21 19:59:38 +02:00
coolneng 18ffbf9a75
Add v_call and j_call to sequence ID 2021-04-21 18:51:08 +02:00
coolneng 82fdfdc6b9
Exchange pattern and subject in the alignment 2021-04-08 18:31:50 +02:00
coolneng dd9f7ffde4
Remove redundant HVR sequence construction 2021-04-07 19:49:44 +02:00
coolneng e694ee3292
Select the first sequence matching the identifier 2021-04-07 18:41:14 +02:00
coolneng e5a7b726a9
Add v_segments and j_segments objects 2021-04-07 18:32:58 +02:00
coolneng 38b35f7d12
Align full sequences efficiently 2021-04-07 18:31:39 +02:00
coolneng f81e4af94e
Amplify VDJ sequences to simplify parsing 2021-03-29 22:57:36 +02:00
coolneng 576597cb04
Remove redundant sequencing runs argument 2021-03-29 20:40:01 +02:00
coolneng 13f453718d
Implement HVR sequence alignment 2021-03-27 09:39:59 +01:00
coolneng 3a10380d8c
Construct a dataframe containing the HVR region 2021-03-25 21:53:49 +01:00
coolneng 8f5b9ee698
Parse curesim and VDJ sequences from files 2021-03-23 20:54:31 +01:00
coolneng 66b39485a9
Save vdj alignment sequences to a CSV 2021-03-23 19:35:10 +01:00
coolneng 97b8914cd5
Add literate programming notebook 2021-03-23 18:24:12 +01:00
coolneng bc666a37c7
Delete CuReSim log file after execution 2021-03-11 21:28:58 +01:00
coolneng d5bf8f3b72
Remove redundant casting 2021-03-11 21:28:00 +01:00
coolneng 762791829a
Save v_call and j_call to a text file 2021-03-11 21:03:16 +01:00