Owner
openvax
9 indexed repositories · View on GitHub
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pyensembl
Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
Python · 408 stars
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mhcflurry
Peptide-MHC I binding affinity prediction
Python · 275 stars
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gtfparse
Parsing tools for GTF (gene transfer format) files
Python · 129 stars
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mhctools
Python interface to running command-line and web-based MHC binding predictors
Python · 104 stars
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varcode
Library for manipulating genomic variants and predicting their effects
Python · 87 stars
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vaxrank
Ranked vaccine peptides for personalized cancer immunotherapy
Python · 67 stars
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topiary
Predict mutated T-cell epitopes from sequencing data
Python · 30 stars
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isovar
Assembly of RNA reads to determine the effect of a cancer mutation on protein sequence
Python · 26 stars
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datacache
Helpers for transparently downloading datasets
Python · 5 stars
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Difficulty 3/5 1-2 days Newbie friendliness 68/100
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Difficulty 4/5 3-5 days Newbie friendliness 52/100
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Difficulty 5/5 Over a week Newbie friendliness 25/100
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Difficulty 5/5 Over a week Newbie friendliness 42/100
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Difficulty 5/5 Over a week Newbie friendliness 25/100
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Difficulty 4/5 3-5 days Newbie friendliness 45/100
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Reconcile nominated large indel and SV interpretations using RNA assemblies and read-path evidence Open
Difficulty 5/5 Over a week Newbie friendliness 25/100
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Difficulty 5/5 Over a week Newbie friendliness 25/100
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Difficulty 4/5 3-5 days Newbie friendliness 58/100
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Difficulty 5/5 Over a week Newbie friendliness 32/100
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Difficulty 5/5 Over a week Newbie friendliness 35/100
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Difficulty 2/5 1-3 hours Newbie friendliness 86/100
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Difficulty 5/5 Over a week Newbie friendliness 35/100
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Difficulty 2/5 1-3 hours Newbie friendliness 88/100
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Difficulty 4/5 3-5 days Newbie friendliness 48/100
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Difficulty 4/5 3-5 days Newbie friendliness 48/100
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Difficulty 4/5 3-5 days Newbie friendliness 52/100
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Difficulty 4/5 3-5 days Newbie friendliness 48/100
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Difficulty 2/5 1-3 hours Newbie friendliness 68/100
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Replace reused nearest processing negatives with seeded probabilistic matching without replacement Open
Difficulty 5/5 Over a week Newbie friendliness 35/100
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v2-2020 full candidate fails presentation gate; component swaps localize most loss to processing Open
Difficulty 5/5 Over a week Newbie friendliness 25/100
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Difficulty 3/5 1-2 days Newbie friendliness 68/100
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Difficulty 4/5 3-5 days Newbie friendliness 55/100
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Difficulty 3/5 1-2 days Newbie friendliness 68/100
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Difficulty 4/5 3-5 days Newbie friendliness 52/100
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Difficulty 4/5 3-5 days Newbie friendliness 45/100
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Difficulty 4/5 3-5 days Newbie friendliness 45/100
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Two different rules decide which args are internal; the report and the run summary can disagree Open
Difficulty 3/5 1-2 days Newbie friendliness 55/100
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Difficulty 2/5 1-3 hours Newbie friendliness 84/100
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Difficulty 4/5 3-5 days Newbie friendliness 48/100
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Difficulty 5/5 Over a week Newbie friendliness 42/100
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Difficulty 5/5 Over a week Newbie friendliness 35/100
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Difficulty 3/5 1-2 days Newbie friendliness 76/100
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Difficulty 4/5 3-5 days Newbie friendliness 48/100
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Difficulty 3/5 1-2 days Newbie friendliness 72/100
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Difficulty 4/5 3-5 days Newbie friendliness 48/100
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Difficulty 4/5 3-5 days Newbie friendliness 68/100
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Difficulty 3/5 1-2 days Newbie friendliness 65/100
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Difficulty 4/5 3-5 days Newbie friendliness 52/100
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Difficulty 5/5 Over a week Newbie friendliness 38/100
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Difficulty 2/5 1-3 hours Newbie friendliness 78/100
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Difficulty 4/5 3-5 days Newbie friendliness 52/100
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Difficulty 4/5 3-5 days Newbie friendliness 52/100
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mhcflurry-downloads: --verbose is a no-op, --quiet still prints progress, info output formatting Open
Difficulty 3/5 1-2 days Newbie friendliness 62/100
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Common CLI mistakes (missing file/column/models dir, bad allele/peptide/flag) end in tracebacks Open
Difficulty 4/5 3-5 days Newbie friendliness 55/100
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Difficulty 4/5 3-5 days Newbie friendliness 64/100
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Difficulty 4/5 3-5 days Newbie friendliness 48/100
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mhcflurry-predict and predict-scan write progress lines to stdout, corrupting redirected CSV output Open
Difficulty 2/5 1-3 hours Newbie friendliness 90/100
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Difficulty 5/5 Over a week Newbie friendliness 35/100
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UCSC unplaced contigs (chrUn_gl000216) aren't mapped, and one aborts annotation of the whole VCF Open
Difficulty 4/5 3-5 days Newbie friendliness 68/100
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