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183 tutorial immunopeptidomics #188

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merged 10 commits into from
Aug 4, 2024
Merged

183 tutorial immunopeptidomics #188

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7b7c7fd
#183 init the hla tutorial
jalew188 Jul 16, 2024
ed5cd2a
#183 add immunopeptidomics tutorial in sphix rst
jalew188 Jul 16, 2024
3c30857
add test
wahlema Jul 18, 2024
a77b2fe
tutorial
wahlema Jul 18, 2024
3286f7b
Finished library prediction
wahlema Jul 19, 2024
503ca25
include protein annotation
wahlema Jul 22, 2024
dc0326c
#183 ruff reformat
jalew188 Jul 23, 2024
d500554
#183 hla tutorial move fasta to cur folder
jalew188 Jul 23, 2024
a2cff73
some types
jalew188 Jul 23, 2024
7d90381
#183 to make tests work
jalew188 Jul 23, 2024
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5 changes: 0 additions & 5 deletions docs/nbs/tutorial_HLA_prediction.rst
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2 changes: 1 addition & 1 deletion docs/notebooks.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -6,10 +6,10 @@ Tutorials and notebooks about how to use AlphaPeptDeep
.. toctree::
:maxdepth: 1

tutorials/tutorial_immunopeptidomics
nbs/tutorial_models_from_scratch
nbs/tutorial_speclib_from_fasta
nbs/alphapeptdeep_hdf_to_tsv
nbs/tutorial_HLA_prediction
nbs/tutorial_model_manager
nbs/tutorial_building_rt_model
nbs/tutorial_building_ccs_model
9 changes: 9 additions & 0 deletions docs/tutorials/example.fasta
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@@ -0,0 +1,9 @@
>tr|A0A024R161|A0A024R161_HUMAN Guanine nucleotide-binding protein subunit gamma OS=Homo sapiens GN=DNAJC25-GNG10 PE=3 SV=1
MGAPLLSPGWGAGAAGRRWWMLLAPLLPALLLVRPAGALVEGLYCGTRDCYEVLGVSRSA
GKAEIARAYRQLARRYHPDRYRPQPGDEGPGRTPQSAEEAFLLVATAYETLKVSQAAAEL
QQYCMQNACKDALLVGVPAGSNPFREPRSCALL
>tr|A0A024RAP8|A0A024RAP8_HUMAN HCG2009644, isoform CRA_b OS=Homo sapiens GN=KLRC4-KLRK1 PE=4 SV=1
MGWIRGRRSRHSWEMSEFHNYNLDLKKSDFSTRWQKQRCPVVKSKCRENASPFFFCCFIA
VAMGIRFIIMVTIWSAVFLNSLFNQEVQIPLTESYCGPCPKNWICYKNNCYQFFDESKNW
YESQASCMSQNASLLKVYSKEDQDLLKLVKSYHWMGLVHIPTNGSWQWEDGSILSPNLLT
IIEMQKGDCALYASSFKGYIENCSTPNTYICMQRTV
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