openvax/topiary issues and pull requests

#89 - ValueError: Invalid contig name 'chr1' for reference 'GRCh38

Issue - State: open - Opened by pswetha over 2 years ago

#88 - The meaning of contains_mutant_residues

Issue - State: open - Opened by ysbioinfo almost 6 years ago

#87 - Request for inclusion of wild-type peptide binding affinity

Issue - State: open - Opened by ARChakravarthy about 6 years ago

#86 - Permission denied or got an unexpected keyword argument 'models_path'

Issue - State: closed - Opened by GSDenghj over 6 years ago - 2 comments

#85 - add --protein-change commandline arg

Pull Request - State: closed - Opened by iskandr over 6 years ago

#84 - Refactor for protein sequences

Pull Request - State: closed - Opened by iskandr over 6 years ago - 1 comment

#83 - Move to OpenVax organization

Pull Request - State: closed - Opened by tavinathanson over 6 years ago - 1 comment

#82 - Namedtuples -> Objects

Pull Request - State: closed - Opened by iskandr almost 7 years ago - 2 comments

#81 - TopiaryPredictor

Pull Request - State: closed - Opened by iskandr almost 7 years ago - 2 comments

#80 - Request for Abbreviated HTML parameter/output

Issue - State: open - Opened by mikekubal almost 7 years ago

#79 - BLAST epitopes against reference proteome

Issue - State: open - Opened by iskandr almost 7 years ago - 1 comment

#78 - Get rid of "wildtype ligandome" dictionary

Issue - State: open - Opened by iskandr almost 7 years ago

#77 - Issue locating NetMHCpan

Issue - State: closed - Opened by ARChakravarthy almost 7 years ago - 1 comment

#76 - reorganizing commandline interface to resemble mhctools and other hammerlab Python tools

Pull Request - State: closed - Opened by iskandr about 7 years ago - 5 comments

#75 - Error in running topiary

Issue - State: open - Opened by bbhinder about 7 years ago

#74 - Error: missing binding predictions

Issue - State: open - Opened by kevin199011 about 7 years ago - 4 comments

#73 - Adding a short RELEASING.md

Pull Request - State: closed - Opened by julia326 over 7 years ago - 1 comment

#72 - Upping mhctools dependency version, also topiary version for release.

Pull Request - State: closed - Opened by julia326 over 7 years ago - 2 comments

#71 - Add a RELEASING.md

Issue - State: closed - Opened by julia326 over 7 years ago - 1 comment

#70 - ValueError: Expected 484916 peptide predictions but got 267878

Issue - State: open - Opened by ihodes over 7 years ago - 1 comment
Labels: bug

#69 - Topiary import error

Issue - State: closed - Opened by ihodes over 7 years ago - 1 comment
Labels: bug

#68 - Grant owner access to hammerlab on pypi

Issue - State: closed - Opened by armish over 7 years ago - 2 comments
Labels: help wanted

#67 - Import normalize_allele_name from mhcnames instead mhctools

Pull Request - State: closed - Opened by armish over 7 years ago - 4 comments

#66 - Updated to work with mhctools 1.0.0

Pull Request - State: closed - Opened by iskandr over 7 years ago - 1 comment

#65 - Cannot run Topairy on my dataset.

Issue - State: open - Opened by Akado2009 over 7 years ago - 4 comments

#64 - Fixing test after netMHCpan 2.8 -> 3.0 update.

Pull Request - State: closed - Opened by julia326 over 7 years ago - 1 comment

#63 - Test failing after netMHCpan update

Issue - State: closed - Opened by julia326 over 7 years ago

#62 - Optionally use isovar to construct coding/protein sequence

Issue - State: open - Opened by iskandr about 8 years ago - 4 comments

#61 - self-ligandome filter fails when unusual alleles have epitopes

Issue - State: closed - Opened by kippakers about 8 years ago - 1 comment

#60 - Removed argparsing code for pMHC prediction and variant loading

Pull Request - State: closed - Opened by iskandr about 8 years ago - 2 comments

#59 - 'Namespace' object has no attribute 'rna_gene_fpkm_file'

Issue - State: closed - Opened by cedarice over 8 years ago - 2 comments

#58 - Wildtype peptide sequence

Issue - State: open - Opened by iskandr over 8 years ago

#57 - Cleaned up commandline arguments

Pull Request - State: closed - Opened by iskandr over 8 years ago - 5 comments

#56 - VCF annotation

Issue - State: open - Opened by serge2016 over 8 years ago - 9 comments

#55 - Question: How are frameshifts handled?

Issue - State: closed - Opened by kippakers over 8 years ago - 2 comments

#54 - Trim protein sequences to not include stop codons

Pull Request - State: closed - Opened by iskandr over 8 years ago - 1 comment

#53 - Peptides with * in sequence causing trouble (with netMHCcons)

Issue - State: closed - Opened by kippakers over 8 years ago - 8 comments

#52 - Make sure we'll correctly translating chr13 g.5864876_5864877insG (mm10)

Issue - State: closed - Opened by iskandr over 8 years ago - 4 comments

#51 - Error of unknown origin

Issue - State: closed - Opened by kippakers over 8 years ago - 9 comments

#50 - Add version

Pull Request - State: closed - Opened by tavinathanson over 8 years ago - 4 comments

#49 - Replace "self-ligandome" filtering with just search over the full proteome

Issue - State: open - Opened by iskandr over 8 years ago - 5 comments

#48 - Don't seem to be filtering stop-gain variants

Issue - State: open - Opened by iskandr over 8 years ago - 4 comments

#47 - NCBIM37

Issue - State: closed - Opened by gmicevic over 8 years ago - 4 comments

#46 - Update README.md

Pull Request - State: closed - Opened by tavinathanson over 8 years ago - 2 comments

#45 - Clarify what NetMHC* versions are supported

Issue - State: open - Opened by tavinathanson over 8 years ago
Labels: enhancement

#44 - Change default NetMHC implementation to NetMHC4 in mhctools

Issue - State: closed - Opened by iskandr over 8 years ago - 1 comment

#43 - Needs a DOI for citations

Issue - State: closed - Opened by iskandr over 8 years ago

#42 - Invalid percentile rank epitopes

Issue - State: open - Opened by rschenck over 8 years ago - 5 comments

#41 - Topiary w/ NetMHC Fails

Issue - State: open - Opened by JPFinnigan almost 9 years ago - 13 comments

#40 - Added option to read transcript FPKM values from StringTie GTF file

Pull Request - State: closed - Opened by iskandr almost 9 years ago - 4 comments

#39 - Handling StringTie .gtf files

Issue - State: closed - Opened by JPFinnigan almost 9 years ago - 3 comments

#38 - Improve RNA loading

Pull Request - State: closed - Opened by iskandr almost 9 years ago - 2 comments

#37 - Fix readthedocs build

Issue - State: open - Opened by iskandr almost 9 years ago - 6 comments

#36 - output Core from netmhciipan

Issue - State: open - Opened by kippakers about 9 years ago - 2 comments

#35 - Integrating multiple predictions per peptide

Issue - State: open - Opened by iskandr about 9 years ago

#34 - Add tests for fields of EpitopePrediction

Issue - State: open - Opened by iskandr about 9 years ago

#33 - Added filtering by self ligandome, minor refactoring

Pull Request - State: closed - Opened by iskandr about 9 years ago - 11 comments

#32 - Add the topiary script to the user's path during topiary installation

Issue - State: open - Opened by tavinathanson about 9 years ago
Labels: enhancement

#31 - Add coveralls to Topiary

Pull Request - State: closed - Opened by tavinathanson about 9 years ago - 1 comment

#30 - Add Python 3.4 back, now that PyEnsembl works

Pull Request - State: closed - Opened by tavinathanson about 9 years ago - 1 comment

#29 - mhcIIpan only outputs 1 allele

Issue - State: closed - Opened by kippakers about 9 years ago - 2 comments

#28 - fix expected commandline arg type for reference-name

Pull Request - State: closed - Opened by iskandr about 9 years ago - 2 comments

#27 - Get Travis running on Python3

Issue - State: closed - Opened by tavinathanson about 9 years ago - 2 comments
Labels: bug

#26 - Add NetMHCIIpan to topiary

Pull Request - State: closed - Opened by tavinathanson about 9 years ago - 2 comments

#25 - Get Topiary running on Travis

Pull Request - State: closed - Opened by tavinathanson about 9 years ago - 2 comments

#24 - mutant_epitope_predictor.epitopes_from_variants needs a test

Issue - State: open - Opened by tavinathanson about 9 years ago
Labels: bug

#23 - wrong version for mhctools in requirements.txt

Pull Request - State: closed - Opened by iskandr about 9 years ago - 1 comment

#22 - Simplify the topiary script by moving most arg-guided logic into the package

Pull Request - State: closed - Opened by iskandr about 9 years ago - 5 comments

#21 - Add unit tests for loading variant collections from JSON

Issue - State: closed - Opened by iskandr about 9 years ago

#20 - Added reference name argument, NetMHC predictor and loading Varcode JSON variant files

Pull Request - State: closed - Opened by iskandr about 9 years ago - 1 comment

#19 - Add --variant option to specify variants directly on the commandline

Pull Request - State: closed - Opened by timodonnell about 9 years ago - 2 comments

#18 - write proper HTML output

Issue - State: open - Opened by timodonnell about 9 years ago

#17 - include commandline arguments used to invoke topiary in HTML output

Issue - State: open - Opened by timodonnell about 9 years ago

#16 - consider exposing topiary as a web service

Issue - State: open - Opened by timodonnell about 9 years ago

#15 - RNA filtering: check that the variant transcript is expressed

Issue - State: open - Opened by timodonnell about 9 years ago - 1 comment

#14 - Add NetMHCIIpan as a predictor

Issue - State: closed - Opened by iskandr about 9 years ago - 2 comments

#13 - Get Topiary working with mice

Issue - State: closed - Opened by tavinathanson about 9 years ago - 1 comment
Labels: enhancement

#12 - Topiary requires pandas >= 0.13.1, however it uses 0.15 functionality

Issue - State: closed - Opened by tavinathanson over 9 years ago - 1 comment
Labels: bug

#11 - Is there a way to pass in the reference/release when it can't be infered

Issue - State: closed - Opened by tavinathanson over 9 years ago - 2 comments

#10 - --skip-variant-errors doesn't always work

Issue - State: open - Opened by kippakers over 9 years ago - 1 comment

#9 - Update padding requirements to fix #8

Pull Request - State: closed - Opened by tavinathanson over 9 years ago - 8 comments
Labels: enhancement

#8 - Padding around mutation doesn't always obey user's request

Issue - State: closed - Opened by tavinathanson over 9 years ago

#7 - Add tab completion for command-line arguments

Issue - State: open - Opened by hammer over 9 years ago

#6 - Add LICENSE

Issue - State: closed - Opened by hammer over 9 years ago - 1 comment

#5 - 'NetMHCpan' object has no attribute '_check_hla_alleles'

Issue - State: closed - Opened by tavinathanson over 9 years ago - 4 comments
Labels: bug, invalid

#4 - moved logic from init.py to Predictor class

Pull Request - State: closed - Opened by iskandr over 9 years ago - 2 comments

#3 - High priority effects

Pull Request - State: closed - Opened by tavinathanson over 9 years ago - 4 comments

#2 - specify library dependency ranges

Pull Request - State: closed - Opened by iskandr over 9 years ago - 1 comment

#1 - Rename library to varmint, adopt adorable mascot

Issue - State: closed - Opened by iskandr over 9 years ago - 1 comment

GitHub / openvax/topiary issues and pull requests