Code

Rmmiller rescue and resolve#113

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bj8th merged 83 commits intomainsheynkman-lab/Long-Read-Proteogenomics:mainfrom rmmiller_rescueAndResolvesheynkman-lab/Long-Read-Proteogenomics:rmmiller_rescueAndResolveCopy head branch name to clipboardDec 14, 2020

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Commits

Commits on Nov 7, 2020

• Adds author name in README.md

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• Adds author name in README.md

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• Deletes temp file

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• Adds author name in README.md

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• Adds Author Name in README (#15)

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• add long read info basics

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• gui app manifest gitignore fix

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• Merge pull request #24 from sheynkman-lab/rmillikinBranch

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• Adds @trishorts name in README.md (#18)

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• Adds @gsheynkman name to README.md (#16)

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• Adds Rachel Miller to the author names in the README (#14)

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• added author and ORCID (#12)

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Commits on Nov 8, 2020

• Refined database orig code (#29)

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• Bj8th orf calling (#25)

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• Adds nextflow files and folders based on nf-core template (#26)

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• added pull scripts from the zenodo site

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• weighted protein inference

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• fixes

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• remove script to hopefully avoid merge conflict..

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• update mzLib

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• require equal long read weight for indistinguishable proteins

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• add contrib

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• Modified README.md File in LR_TranscriptomeSummary

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• Merge pull request #37 from sheynkman-lab/dev_rmillikin

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• Add files via upload

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• update main readme with author names (#38)

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• fix minor errors in readme (#40)

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• excel compatible tsv by default

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• accept thermo license by default

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• Merge pull request #42 from sheynkman-lab/dev_rmillikin

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Commits on Nov 9, 2020

• Updated READMEs, uploaded scripts for isoform mapping, protein clustering. (#41)

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Commits on Nov 10, 2020

• updated contributions (#44)

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• Attempt to create a container for blast mapping process within nextflow. (#48)

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• adding cpat and transdecoder containers (#36)

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• Update README.md

  kyuubi430

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• Updated version of previous files with less typos

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• Delete Transcriptomic_Proteomic_Comparison.ipynb

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• Delete m_MMprocess.py

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• Delete m_gen_maps.py

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• Delete m_make_gene_length_table.py

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• Delete m_sqantitable.py

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• Delete m_squantitable.py

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• Updated version with less typos

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• Update README.md

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• Preliminary module for analyzing peptide space

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Commits on Nov 11, 2020

• Added commands to run CPAT. 'output' directory to .gitignore. (#53)

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• Add nextflow-related files, sundries. (#55)

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• Adding Simi's transcriptomic and peptide analysis scripts. (#56)

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• argparse modification (#57)

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• adds lr_orfcalling.nf and lr_orfcalling_nextflow.config in the module LR_ORFCalling (#59)

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Commits on Nov 15, 2020

• Protein Inference Analysis Module Custom Script (#64)

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• Add files via upload

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• Need to merge with latest dev (disregarding differences in dev_gloria, which are outdated) (#67)

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• Merge branch 'dev' into kyuubi430-this-is-what-I-am-doing-dev

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• Convert jupyter notebook into python

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Commits on Nov 16, 2020

• ORF Calling - bug fix (#70)

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  gsheynkman

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• Update README.md (#65)

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Commits on Nov 17, 2020

• ORF Filtering bug fixes and RefineDB (#71)

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Commits on Nov 18, 2020

• Adds Dockerfile, environment.yml for SQANTI3 (#72)

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• Updated peptide_analysis script for review and added required files/tables

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• Update peptide_analysis.py

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• Updated .gitignore with a local data file

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• Updated peptide_analysis.py to include new path info

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• Delete gene_based_info.tsv

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• Delete trans_to_gene.tsv

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• Updated peptide analysis file (#66)

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Commits on Nov 21, 2020

• 6frm readme (#45)

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• Protein Inference (#74)

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• Removed unnecessary files from Transcriptome Module

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• Removed unnecessary files from Transcriptome module

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• Removed unnecessary files from Transcriptome module

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• Removed unnecessary files from Transcriptome module

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• Removed unnecessary files from Transcriptome module (#75)

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Commits on Nov 22, 2020

• Merge branch 'kyuubi430-this-is-what-I-am-doing-dev' into dev

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Commits on Nov 24, 2020

• Simi and Gloria - Update referencetable, transcriptome, and peptide modules (#78)

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• Adds modules nextflow pseudocode (#79)

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Commits on Nov 25, 2020

• Dev rmmiller protein inference (#83)

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Commits on Dec 14, 2020

• rescue algorithm implemented

  rmmiller22

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• merge branches (rescue and main)

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• gerge branch 'main_merge' into rmmiller_rescueAndResolve

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• eliminate added conflict files

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• config file remove

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• spelling fix

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