sheynkman-lab Long-Read-Proteogenomics issues

sheynkman-lab / Long-Read-Proteogenomics

A workflow for enhanced protein isoform detection through integration of long-read RNA-seq and mass spectrometry-based proteomics.

MIT License

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issues

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Not described SQANTI protein categories

#172 pclavell opened 1 month ago
0
Singularity container?

#170 YichaoOU closed 1 year ago
4
Error with demo data in 'mass_spec_raw_convert'

#169 almart7 opened 1 year ago
2
metamorpheus and rescue+resolve

#168 rsalz opened 1 year ago
0
pNNC from NIC transcript

#167 rsalz closed 1 year ago
2
[WIP] Implement easier singularity compatibility

#166 dnwissel opened 1 year ago
0
[singularity] Adding `--writable-tmpfs` option to selected containers for Singularity compatibility

#165 dnwissel opened 1 year ago
0
Error downloading dependencies

#164 rsalz closed 1 year ago
1
Error running ref_table_generation.nf

#163 MayankMurali closed 1 year ago
1
Short read data requirement

#162 rsalz closed 1 year ago
1
File/Column naming conventions

#161 Sktbanerjee1 opened 1 year ago
0
No full splice matches in protein classification

#160 tabeariepe closed 1 year ago
3
git clone line issue

#159 maallen3 closed 2 years ago
3
added rename_cds_to_exon and sqanti3_protein

#158 bj8th closed 2 years ago
0
missing rename_cds_to_exon.py and sqanti3_protein.py scripts

#157 tabeariepe closed 2 years ago
1
Increases DOI badge size in the README

#156 cgpu closed 2 years ago
0
For each of the modules, add a shell script as was done in generate_reference_tables

#155 adeslatt opened 2 years ago
0
Adds CI trigger for push to important branches [main, dev]

#154 cgpu closed 2 years ago
1
DO NOT MERGE Yet: Updating with smaller star_genome.tar.gz for testing and vignettes

#153 adeslatt closed 3 years ago
2
Adeslatt updates zenodo

#152 cgpu closed 3 years ago
0
Consider further subsampling test data (used in configs)

#151 cgpu closed 3 years ago
0
Minor refactor of --metamorpheus_toml [debugs cloud execution]

#150 cgpu closed 3 years ago
4
Docs

#149 bj8th closed 3 years ago
0
Delete branch.yml

#148 cgpu closed 3 years ago
0
Sheynkman lab main

#147 adeslatt closed 3 years ago
0
Is uniprot_fasta still a valid parameter?

#146 adeslatt opened 3 years ago
0
Bj8th

#145 bj8th closed 3 years ago
0
metamorpheus optional toml file implemented

#144 bj8th closed 3 years ago
0
This creates the accounting for running from Zenodo dealing with the two folders mass_spec and star_genome

#143 adeslatt closed 3 years ago
0
Folders to tar.gz - need to create two inputs - one for mass_spec_raw and one for mass_spec_mzml

#142 adeslatt closed 3 years ago
0
Removing `docs`

#141 adeslatt opened 3 years ago
0
Scripts to download from AWS and upload to Zenodo, documentation regarding the process in AWStoZenodo.md.

#140 adeslatt closed 3 years ago
0
Idea for visualizing protein groups

#139 gsheynkman closed 3 years ago
1
Nextflow edits gloria may22

#138 gsheynkman closed 3 years ago
0
Went over Ben's pipeline, Gloria added minor edits.

#137 bj8th closed 3 years ago
1
Bj8th protein db

#136 bj8th closed 3 years ago
0
Patch to enable large file deletion from git history

#135 cgpu closed 3 years ago
0
DO NOT MERGE - For comparison purposes only

#134 cgpu closed 3 years ago
0
Remove large file from commit history

#133 gsheynkman closed 3 years ago
1
Enables use of 1 param runs with --config

#132 cgpu closed 3 years ago
1
Adds accession mapping and protein group compare code

#131 gsheynkman closed 3 years ago
0
Gloria dev

#130 gsheynkman closed 3 years ago
0
Gloria dev

#129 bj8th closed 3 years ago
0
Adds accmapping module final code

#128 gsheynkman closed 3 years ago
1
Adds accmapping module final code

#127 gsheynkman closed 3 years ago
0
Nextflow MetaMorpheus

#126 bj8th closed 3 years ago
1
Bj8th nextflow

#125 bj8th closed 3 years ago
0
Upload Gencode and PacBio MM ProteinGroups file to Zenodo.

#124 gsheynkman closed 3 years ago
0
Redundant entries in refined datbase output

#123 gsheynkman closed 3 years ago
0
Figure out how others can upload to the LRP Zenodo

#122 gsheynkman closed 3 years ago
0