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52 Commits 1 Branch 5 Tags 213 KiB
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52 Commits

Author SHA1 Message Date
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
coolneng 7b15df7614
Simplify repertoire generation 2021-03-10 12:34:20 +01:00
coolneng f4a001f821
Change CuReSim output file extension to FASTQ 2021-03-10 12:33:25 +01:00
coolneng d2e45bc00f
Change output format to FASTA 2021-03-02 20:08:14 +01:00
coolneng deb1066982
Set CuReSim read size to 350 bases 2021-03-02 20:07:05 +01:00
coolneng edc4a72425
Update gitignore 2021-02-28 02:24:23 +01:00
coolneng 42aadb1e28
Add sequencing runs CLI argument 2021-02-28 02:23:58 +01:00
coolneng ae5014fd74
Remove a_chain generation 2021-02-28 02:23:28 +01:00
coolneng 34722f3ebf
Add gitignore 2021-02-26 03:11:34 +01:00
coolneng b51706d0c0
Create a script that executes the pipeline 2021-02-26 03:11:25 +01:00
coolneng 53dda36c66
Export the data to FASTQ files 2021-02-26 02:20:11 +01:00
coolneng b035c496f7
Filter the relevant columns from immuneSIM output 2021-02-26 02:19:40 +01:00
coolneng 2cece5e53e
Set number of sequences via a CLI argument 2021-02-25 20:02:11 +01:00
coolneng 010849d4c9
Generate both alfa and beta chains 2021-02-25 20:00:35 +01:00
coolneng f63fabac4f
Add development tools as project dependencies 2021-02-22 21:40:17 +01:00
coolneng 5c37fad320
Add data directories 2021-02-22 00:59:32 +01:00