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mskcc
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neoantigen-pipeline
Pipeline for computing neoantigen qualities from DNA and RNA-Seq data
MIT License
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Add tsv output using the new json to tsv module
#54
nikhil
opened
2 days ago
1
Update nextflow.config
#53
nikhil
closed
2 weeks ago
1
Update usage.md
#52
johnoooh
opened
2 weeks ago
1
Dev
#51
nikhil
closed
1 month ago
1
Feature/update modules to base develop
#50
nikhil
closed
1 month ago
1
Dev
#49
nikhil
closed
1 month ago
1
Update input for test config
#48
nikhil
closed
1 month ago
1
fix download_pipeline test
#47
nikhil
closed
1 month ago
2
Release candidate for 1.0.0
#46
nikhil
closed
1 month ago
1
Feature/netmhc refactor
#45
nikhil
closed
2 months ago
2
Feature netmhc refactor and bug fixes
#44
nikhil
closed
3 months ago
1
Document output for neoantigen pipeline
#43
nikhil
opened
3 months ago
0
Test neosv with example bedpe file
#42
nikhil
opened
3 months ago
0
neosv fasta output
#41
nikhil
opened
3 months ago
0
Handle ids in fasta
#40
nikhil
opened
4 months ago
1
Refactor netmhcpanandstab steps
#39
nikhil
opened
4 months ago
0
Add netmhcstabpan stability scores
#38
nikhil
opened
4 months ago
0
Update README.md
#37
johnoooh
closed
5 months ago
1
PR for MVP release! (for real)
#36
nikhil
closed
5 months ago
2
PR for MVP release!
#35
nikhil
closed
5 months ago
0
Adding netmhcpan
#34
johnoooh
closed
5 months ago
0
Input schema changes from nf-core default to new schema
#33
johnoooh
closed
5 months ago
1
Subworkflows merge test
#32
johnoooh
closed
5 months ago
1
Adding subworkflows and updating modules to be in line with current modules repo
#31
johnoooh
closed
5 months ago
0
Fix linting for neoantigenEditing computefitness
#30
nikhil
opened
5 months ago
0
Python script to annotate NMD
#29
nikhil
opened
5 months ago
1
Add module for netmhcpanstab
#28
nikhil
closed
5 months ago
0
Nonsense mediated decay
#27
johnoooh
opened
5 months ago
0
neosplice
#26
nikhil
opened
5 months ago
0
netmhcstab vs netmhcstabpan?
#25
nikhil
closed
5 months ago
1
Add workflow for neonantigenediting
#24
nikhil
closed
5 months ago
0
Add workflow for phylowgs
#23
nikhil
closed
5 months ago
0
investigate lens and find out what tools can be integrated into version 2
#22
nikhil
opened
5 months ago
5
What should we name the pipeline?
#21
nikhil
opened
6 months ago
2
Check neoantigen editing if folder structure is needed in data for patient data
#20
nikhil
closed
5 months ago
0
wish list for version 2
#19
nikhil
opened
6 months ago
1
end to end testing
#18
nikhil
closed
5 months ago
1
Nextflow module for Neoantigen editing - compute_fitness.py
#17
nikhil
closed
5 months ago
0
Nextflow module for Neoantigen editing - align_neoantigens_to_IEDB.py
#16
nikhil
closed
5 months ago
1
Create nextflow module for aggregate inputs
#15
nikhil
closed
5 months ago
0
nextflow module for phylo_wgs write_results
#14
nikhil
closed
5 months ago
1
nextflow module for pyhlo_wgs multievolve
#13
nikhil
closed
5 months ago
1
Nextflow module for phylo_wgs create_phylowgs_inputs.py
#12
nikhil
closed
6 months ago
2
Nextflow module for phylo_wgs parse_cnvs
#11
nikhil
closed
6 months ago
2
Initialize neoantigen nextflow pipeline
#10
nikhil
closed
6 months ago
1
Create a script to map out Phylowgs to Greenbaum tools
#9
nikhil
closed
5 months ago
1
Neoantigen input to greenbaum tools
#8
nikhil
closed
6 months ago
2
Test Neoantigen Editing with their test inputs
#7
nikhil
closed
6 months ago
1
Investigate Neoantigen tools/pipelines
#6
nikhil
opened
7 months ago
2
Investigate new Neoantigen tools and pipelines
#5
nikhil
opened
7 months ago
0
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