griffithlab/pVACtools issues and pull requests

#956 - Handle flurry state correctly when running the PostProcessor outside …

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

#955 - Pin latest version of varcode that has no pyvcf dependency and remove pinned setuptools version

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

#954 - Add API status tests to run once a day

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

#953 - Mock netchop and netmhcstabpan API calls during pVACbind tests

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

#952 - Remove support for python 3.6 and add support for 3.11

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

#951 - Ensure that pVACtools 4.0 supports Python 3.11

Issue - State: closed - Opened by susannasiebert over 1 year ago

#950 - Four prediction results(Score, Percentile) in a row not correspond to the same epitope

Issue - State: closed - Opened by RysBen over 1 year ago - 2 comments

#949 - More pVACview tweaks

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

#948 - Update reference proteome analysis to consider patient genotype

Issue - State: open - Opened by malachig over 1 year ago - 3 comments
Labels: grant

#947 - Create helper tool that generates information for a peptide order form

Issue - State: open - Opened by malachig over 1 year ago
Labels: grant

#946 - Fix parsing issue for class II IEDB predictions in pVACbind and pVACfuse

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

#945 - Fix parsing issue for class II IEDB predictions in pVACbind and pVACfuse

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

#944 - Various minor pVACview improvements

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

#943 - When picking the best peptide, deprioritize epitopes that fail the anchor residue check

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

#942 - When picking the best peptide, deprioritize epitopes that fail the anchor residue check

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

#941 - Don't write reference match header again if the input TSV file already contains the column

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

#940 - Should anchor position be a criteria in the aggregate reprot for class II predictions?

Issue - State: open - Opened by susannasiebert over 1 year ago - 1 comment
Labels: grant

#939 - Copy updated metrics file with reference match data into original metrics file location

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

#938 - Various pVACview bug fixes and small feature tweaks

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

#937 - Fix various issues with ref match feature

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

#936 - Add a bit more information when showing classII info in a classI session of pvacview (or the reverse)

Issue - State: closed - Opened by malachig over 1 year ago

#935 - Some more pvacview bugfixes

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

#934 - Ensure tsv suffix for temporary aggregate report output file

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

#933 - Ensure that MT. and WT. will only be removed from beginning of seq ID when extracting the variant index

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

#932 - Catch case where allele-specific anchors are turned on for Class II data

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

#931 - Output transcript attribtues in the correct sort order

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

#930 - Show a list of reference matches in pVACview

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

#929 - fix the missing json import

Pull Request - State: closed - Opened by ndeng1 over 1 year ago

#928 - NNAlign prediction error occurs when running with other prediction methods.

Issue - State: closed - Opened by ndeng1 over 1 year ago - 2 comments

#927 - Pvacview bug fix

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

#926 - Incorporate anchor criteria when selecting the best peptide.

Issue - State: closed - Opened by susannasiebert over 1 year ago

#925 - Add functionality to calculate molecular weights for peptides to be synthesized

Issue - State: closed - Opened by malachig over 1 year ago - 1 comment

#924 - bug fix regarding row highlights

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

#923 - add new pVACview demo files

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

#922 - Add ability to run standalone reference similarity command on aggregate report

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

#921 - pVACview bug fix when anchor parameter is turned on

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

#918 - Write prediction tmp files to the pvacseq run's output tmp directory

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

#917 - Update reference protome similarity step to work with new mutation position format

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

#916 - Mock netchop API calls in pVACbind tests

Issue - State: closed - Opened by susannasiebert over 1 year ago

#915 - Fix some issue with new aggregate report feature on `pvacseq generate_protein_fasta`

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

#914 - Output a list of unsupported NetMHCstabpan alleles

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

#912 - Further improve selection of best epitope in aggregate report

Issue - State: open - Opened by susannasiebert over 1 year ago
Labels: grant

#911 - Add new pVACsplice tool

Pull Request - State: open - Opened by mrichters over 1 year ago - 1 comment

#909 - TSVfile is empty

Issue - State: closed - Opened by dhy2002 over 1 year ago - 2 comments

#907 - Comparison with previous command breaks parallel multi-sample processing

Issue - State: closed - Opened by danilotat over 1 year ago - 3 comments

#906 - Update bug issue template to make use of input fields

Issue - State: closed - Opened by susannasiebert almost 2 years ago

#904 - Bump werkzeug from 2.0.3 to 2.2.3

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#901 - Incorporate better handling of HLA allele-specific expression loss

Issue - State: open - Opened by malachig almost 2 years ago
Labels: grant

#899 - Bump oauthlib from 3.2.0 to 3.2.2

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#894 - Investigate adding support for EpiScan Predictor

Issue - State: open - Opened by malachig almost 2 years ago
Labels: grant

#891 - Bump setuptools from 57.4.0 to 65.5.1 in /docs

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#890 - Bump setuptools from 57.4.0 to 65.5.1

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#888 - Remove unneeded `import vcf` statement

Pull Request - State: closed - Opened by susannasiebert almost 2 years ago

#885 - Simplify parameter setting in pipeline.py and backfill some parameters that weren't getting passed along

Pull Request - State: closed - Opened by susannasiebert almost 2 years ago

#882 - Add read support and coverage metrics, filtering, and tiering to pVACfuse

Pull Request - State: closed - Opened by susannasiebert almost 2 years ago

#881 - Bump certifi from 2021.10.8 to 2022.12.7

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#880 - Add support for screening of end modifications to long peptides to accommodate manufacture/solubility issues

Issue - State: open - Opened by malachig almost 2 years ago - 1 comment
Labels: grant

#878 - Bump pillow from 8.4.0 to 9.3.0

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies

#877 - Bump tensorflow from 2.2.2 to 2.9.3

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies

#871 - Fix bug for handling score columns when only an EL algorithm was run

Pull Request - State: closed - Opened by susannasiebert about 2 years ago

#870 - Always exclude a TSL status of NA for tiering and filtering

Pull Request - State: closed - Opened by susannasiebert about 2 years ago - 3 comments

#866 - A few fixes/improvements to percentiles

Pull Request - State: closed - Opened by susannasiebert about 2 years ago

#863 - Implement a tool/step that identifies peptides that could be toxic

Issue - State: open - Opened by malachig about 2 years ago - 3 comments
Labels: grant

#861 - Update requirements.txt

Pull Request - State: closed - Opened by susannasiebert about 2 years ago

#860 - Support percentiles for MHCnuggets

Pull Request - State: closed - Opened by susannasiebert about 2 years ago

#857 - Indicate in the stdout which alleles were unsupported by NetMHCstabpan.

Issue - State: closed - Opened by susannasiebert about 2 years ago

#847 - Update image files to source from web

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

#833 - Sample header line (starting with "#CHROM") does not start with required prefix #CHROM

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

#829 - Explore incorporation of "Inhibigens" in neoantigen candidate prioritization

Issue - State: open - Opened by malachig over 2 years ago - 1 comment
Labels: grant

#827 - Use MHCgnomes to help resolve HLA alleles

Issue - State: open - Opened by chrisamiller over 2 years ago
Labels: grant

#814 - pip install pvactool=v3.0.0, can not find tensorflow version 2.2.2

Issue - State: closed - Opened by YuntaoTan over 2 years ago - 3 comments

#787 - Add ability to run the reference proteome step on the full peptide sequence in a fasta

Issue - State: open - Opened by susannasiebert over 2 years ago - 2 comments
Labels: grant

#777 - Incorporate DeepNeo for better class II priortization

Issue - State: open - Opened by malachig almost 3 years ago - 1 comment
Labels: grant

#762 - Add retry when calls to standalone IEDB fail

Issue - State: open - Opened by asmlgkj almost 3 years ago - 10 comments

#757 - Add support for proximal inframe indels

Issue - State: open - Opened by susannasiebert almost 3 years ago - 1 comment
Labels: grant

#755 - Incorporate predictions from TCRMatch

Issue - State: open - Opened by malachig almost 3 years ago - 1 comment
Labels: grant

#724 - Filtered and aggregate report interpretation

Issue - State: closed - Opened by rbowenj about 3 years ago - 5 comments

#723 - Reference proteome similarity error

Issue - State: closed - Opened by rbowenj about 3 years ago - 4 comments

#712 - use_2to3 and setuptools 58+ problem

Issue - State: closed - Opened by Stikus about 3 years ago - 8 comments

#709 - Consider use of APE-Gen algorithm

Issue - State: open - Opened by malachig about 3 years ago - 1 comment
Labels: grant

#706 - Investigate use of igv-reports for genomic review of candidates

Issue - State: open - Opened by malachig about 3 years ago - 1 comment
Labels: grant

#703 - Investigate ACME algorithm

Issue - State: open - Opened by malachig about 3 years ago
Labels: grant

#702 - Investigate PUFFIN algorithm

Issue - State: open - Opened by malachig about 3 years ago
Labels: grant

#684 - Investigate new tool GraphSol for predicting peptide solubility

Issue - State: open - Opened by malachig over 3 years ago
Labels: grant

#681 - Calculate HLA-I evolutionary divergence (HED) score

Issue - State: open - Opened by malachig over 3 years ago - 1 comment
Labels: grant

#680 - Incorporate Patient Harmonic-mean Best Rank (PHBR) into class I report

Issue - State: open - Opened by malachig over 3 years ago - 2 comments
Labels: grant

#677 - Add tests for python 3.9

Pull Request - State: closed - Opened by susannasiebert over 3 years ago - 2 comments

#670 - Move stability and cleavage site predictions to the all epitopes report

Issue - State: open - Opened by susannasiebert over 3 years ago - 2 comments

#663 - Spot check transcript vs. gene expression values from kallisto

Issue - State: open - Opened by malachig over 3 years ago
Labels: grant

#652 - Add NetH2pan to the list of supported prediction algorithms

Issue - State: open - Opened by nruthen over 3 years ago - 4 comments
Labels: grant

#644 - Submit Wildtype and Frameshift plugins to VEP.

Issue - State: open - Opened by susannasiebert almost 4 years ago - 2 comments
Labels: grant

#635 - Investigate netmhccons `len(peptide_list) != len(scores)` error

Issue - State: open - Opened by susannasiebert almost 4 years ago

#627 - Investigate steps needed to create a phased VCF of somatic variants only

Issue - State: open - Opened by susannasiebert almost 4 years ago
Labels: documentation, grant

#589 - Have pVACvector output a list of problematic peptides

Issue - State: open - Opened by susannasiebert about 4 years ago - 1 comment
Labels: pVACvector

#525 - Set up singularity distribution

Issue - State: open - Opened by malachig over 4 years ago - 5 comments
Labels: grant

#519 - Add reference proteome Blast step to pVACvector

Issue - State: open - Opened by susannasiebert over 4 years ago - 1 comment
Labels: pVACvector

#513 - Calculate reference proteome similarity when running `generate_protein_fasta` commands

Issue - State: open - Opened by susannasiebert over 4 years ago
Labels: grant

#507 - Rework `filter_response` response method in `lib/prediction_class.py`

Issue - State: open - Opened by jeongmeani over 4 years ago - 11 comments

#481 - Do you plan to add support for HLAthena?

Issue - State: open - Opened by alongalor almost 5 years ago - 3 comments
Labels: grant

#467 - Add support for hmmhc

Issue - State: open - Opened by chrisamiller about 5 years ago
Labels: grant

GitHub / griffithlab/pVACtools issues and pull requests