openvax/mhctools issues and pull requests

#170 - Unable to open(r) file when running netMHCpan --version _MHCTOOLS_VERSION_SNIFFING

Issue - State: open - Opened by trevorpfiz 4 months ago - 4 comments

#169 - NetMHCIIpan4.3 tests failing

Issue - State: open - Opened by iskandr 7 months ago

#168 - added support to NetMHCIIpan 4.3

Pull Request - State: closed - Opened by fkgruber 9 months ago - 5 comments

#167 - Added support for NetMHCstabpan (GH Issue #64)

Pull Request - State: closed - Opened by dhuvik 12 months ago - 2 comments

#166 - Small fix for the NetMHCPan 4.1 support

Pull Request - State: closed - Opened by amitschang over 1 year ago - 1 comment

#165 - Support netmhcpan41

Pull Request - State: closed - Opened by timodonnell over 1 year ago

#164 - Netmhcpan41

Pull Request - State: closed - Opened by amitschang over 1 year ago

#163 - NetMHCpan-4.1 support

Pull Request - State: closed - Opened by denklewer over 3 years ago - 5 comments

#162 - support BERTMHC for class II prediction

Issue - State: open - Opened by timodonnell about 4 years ago

#160 - Propagating --do-not-raise-on-error as a CLI arg for IEDB constructors

Pull Request - State: closed - Opened by julia326 over 4 years ago - 5 comments

#159 - Not crashing if IEDB predictor is missing some predictions

Pull Request - State: closed - Opened by julia326 over 4 years ago - 3 comments

#158 - Adding NetMHCIIpan 4.0 to mhctools

Pull Request - State: closed - Opened by julia326 over 4 years ago - 1 comment

#157 - Install MHCflurry 2.0 by default

Pull Request - State: closed - Opened by iskandr over 4 years ago - 1 comment

#156 - Add support for mhcflurry 2.0 ?

Issue - State: closed - Opened by plsysu over 4 years ago - 5 comments

#155 - Add support for NetCTLpan ?

Issue - State: closed - Opened by plsysu over 4 years ago

#154 - Too many open files

Issue - State: closed - Opened by plsysu over 4 years ago

#153 - set TMPDIR(-tdir) of netMHCpan/netMHCIIpan by command line arguments ?

Issue - State: closed - Opened by plsysu over 4 years ago

#152 - Update output parser for NetMHCpan-4.1 and NetMHCIIpan-4.0

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

#151 - Remove mhcflurry upper version limit

Pull Request - State: closed - Opened by timodonnell almost 5 years ago - 1 comment

#150 - Mhcflurry 1.6.0 support

Issue - State: closed - Opened by Stikus almost 5 years ago - 1 comment

#149 - MixMHCpred not creating mixmhcpred_outputs.txt in tmp dir

Issue - State: open - Opened by zakimolvi almost 5 years ago - 1 comment

#148 - error when peptide contains 'U'

Issue - State: closed - Opened by kevinkovalchik almost 5 years ago - 1 comment

#147 - preserve stdout as part of error for MixMHCpred

Pull Request - State: closed - Opened by iskandr about 5 years ago - 1 comment

#146 - Add MixMHCpred

Pull Request - State: closed - Opened by iskandr over 5 years ago - 2 comments

#145 - Add support for MixMHCPred

Issue - State: closed - Opened by iskandr over 5 years ago

#144 - Support for eluted_ligand mode for NetMHCpan4

Pull Request - State: closed - Opened by timodonnell over 5 years ago - 1 comment

#143 - Update RELEASING.md

Pull Request - State: closed - Opened by timodonnell over 5 years ago - 1 comment

#142 - Add 'elution_score' field to BindingPrediction

Pull Request - State: closed - Opened by timodonnell over 5 years ago - 1 comment

#141 - configure netMHC

Issue - State: open - Opened by sheljoy over 5 years ago - 1 comment

#140 - Add ability to filter results by ic50 or percentile rank in commandline tool

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

#139 - Bump mhcflurry

Pull Request - State: closed - Opened by timodonnell about 6 years ago - 1 comment

#138 - how to install api not in mhctools

Issue - State: closed - Opened by worker000000 about 6 years ago - 1 comment

#137 - ValueError: Response from IEDB is missing 'allele' column: length

Issue - State: closed - Opened by sbwiecko about 6 years ago

#136 - Adding ability to run mhctools CLI with netMHCpan 4.0.

Pull Request - State: closed - Opened by julia326 over 6 years ago - 4 comments

#135 - Add netMHCpan 4.0 as an option

Issue - State: closed - Opened by julia326 over 6 years ago - 1 comment

#134 - Make netmhc-3.4 go through Docker (like netChop)

Issue - State: open - Opened by julia326 over 6 years ago

#133 - NetMHCpan4

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

#132 - Add examples to readme

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

#131 - allow MHCflurry to raise UnsupportedAllele

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

#130 - MHCflurry creates BindindPredictions with None for percentile rank

Issue - State: closed - Opened by iskandr about 7 years ago - 1 comment

#129 - MHCflurry should raise UnsupportedAllele

Issue - State: closed - Opened by iskandr about 7 years ago - 3 comments

#128 - Update to use new IEDB result format

Pull Request - State: closed - Opened by timodonnell about 7 years ago - 4 comments

#127 - capitalize sequences read from FASTAs

Pull Request - State: closed - Opened by timodonnell about 7 years ago - 3 comments

#126 - Add NetMHCpan4 wrapper

Pull Request - State: closed - Opened by timodonnell about 7 years ago - 2 comments

#125 - add support for NetMHCpan 4.0

Issue - State: closed - Opened by timodonnell about 7 years ago - 2 comments

#124 - Add support for mhcflurry percentile ranks and custom MHCflurry models dir

Pull Request - State: closed - Opened by timodonnell about 7 years ago - 2 comments

#123 - Import mhcflurry locally

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

#122 - sniff for multiple dashes in NetMHC4 output file

Pull Request - State: closed - Opened by iskandr over 7 years ago - 3 comments

#121 - Non-deterministic failure from CLI when using NetMHC 4.0

Issue - State: closed - Opened by iskandr over 7 years ago - 2 comments

#120 - problem with netChop

Issue - State: open - Opened by weipenegHU over 7 years ago - 2 comments

#119 - error when using NetMHC

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

#118 - NetMHCpan-2.8 fixes

Pull Request - State: closed - Opened by julia326 over 7 years ago - 4 comments

#117 - Removing some more precision from the MHCflurry result comparison.

Pull Request - State: closed - Opened by julia326 over 7 years ago - 3 comments

#116 - Fixing mhctools test: reducing expected mhcflurry precision

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

#115 - Adding a MANIFEST.in to include the license and README files.

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

#114 - Check peptide inputs always

Pull Request - State: closed - Opened by julia326 over 7 years ago - 4 comments

#113 - Fix doc formatting on PyPi

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

#112 - Fixing ii_pan test to expand DRB to include DRA

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

#111 - Fixing netmhciipan

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

#110 - Add vaxrank unit tests

Pull Request - State: closed - Opened by julia326 over 7 years ago - 5 comments

#109 - Fixing mhcnames version to 0.1.0 temporarily

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

#108 - IOErrors when running multiples processes at once.

Issue - State: open - Opened by alexanderwhatley over 7 years ago

#107 - Set correct min/max peptide lengths for predictors

Pull Request - State: closed - Opened by iskandr over 7 years ago - 8 comments

#106 - Better peptide length error handling

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

#105 - Attempt to fix failing travis build

Pull Request - State: closed - Opened by timodonnell over 7 years ago - 6 comments

#104 - update MHCflurry to take predictor instead of models_dir

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

#103 - Add mhcflurry round2 tim

Pull Request - State: closed - Opened by timodonnell over 7 years ago

#102 - Add mhcflurry support

Pull Request - State: closed - Opened by julia326 over 7 years ago - 5 comments

#101 - Gracefully handle case where user asks for unsupported allele

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

#100 - Group peptides by length for netMHC v3, similar to netMHCcons.

Pull Request - State: closed - Opened by julia326 almost 8 years ago - 2 comments

#99 - Group peptides by length in netmhc3

Issue - State: closed - Opened by julia326 almost 8 years ago

#98 - added -extract-subsequences flag

Pull Request - State: closed - Opened by iskandr almost 8 years ago - 7 comments

#97 - Add CLI option to compute affinity for subsequences

Issue - State: closed - Opened by ihodes almost 8 years ago - 1 comment
Labels: enhancement

#96 - lear

Issue - State: closed - Opened by ghost almost 8 years ago

#95 - make predictors check actual contents of pMHCs and not just lengths

Pull Request - State: closed - Opened by iskandr almost 8 years ago - 3 comments

#94 - Instead of just checking peptide counts, show examples of missing peptides

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

#93 - split netmhccons peptide lists by length

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

#92 - NetMHCcons doesn't work with multiple peptide lengths

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

#91 - predict_peptides should check to make sure it has correct number of predictions

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

#90 - Fix README

Issue - State: closed - Opened by julia326 almost 8 years ago

#89 - raise errors instead of silently returning empty dataframes when running netmhcpan on 7 mers or on peptides with X in them

Issue - State: open - Opened by timodonnell almost 8 years ago

#88 - Close input files after filling, deleted unused input file format

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

#87 - Failure when predicting 11.5M peptides

Issue - State: closed - Opened by iskandr almost 8 years ago - 2 comments

#86 - Refactoring and addition of peptides-only prediction method

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

#84 - NetChop test fails

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

#81 - NetMHCpan missing process_limit

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

#80 - run netMHCpan on multiple alleles at once

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

#79 - tons of defunct netMHCpan processes

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

#75 - added --input-fasta-file argument

Pull Request - State: closed - Opened by iskandr about 8 years ago - 9 comments

#70 - Add CLI argument for list of peptides

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

#69 - NetMHCpan (and probably other predictors) allows a peptide list as input

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

#67 - Fixes mhctools CLI (wrong dataframe method call)

Pull Request - State: closed - Opened by julia326 over 8 years ago - 3 comments

#64 - Add support for NetMHCstabpan

Issue - State: open - Opened by iskandr over 8 years ago - 1 comment
Labels: enhancement

#63 - One logger per module, and some associated changes:

Pull Request - State: closed - Opened by julia326 over 8 years ago - 2 comments

#61 - Fix column indexes for NetMHCIIpan 3.1 parser

Pull Request - State: closed - Opened by jfeala over 8 years ago - 3 comments

#59 - normalize_allele_name in alleles.py with 3 digit allele codes

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

#54 - NetMHCIIpan v3.0 support

Issue - State: closed - Opened by jfeala over 8 years ago - 5 comments

#53 - Error message logged when creating NetMHC

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

#44 - remove epitope_collection and builder and replace with pandas dataframes

Issue - State: closed - Opened by timodonnell over 9 years ago - 3 comments

#43 - the 'fasta_dictionary' argument to a predictor's `predict` method should be renamed

Issue - State: closed - Opened by timodonnell over 9 years ago - 3 comments

GitHub / openvax/mhctools issues and pull requests