coolneng/locigenesis
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Author SHA1 Message Date
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 0.1.0 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
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