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sheynkman-lab
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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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Updates command for SQANTI3
#121
cgpu
closed
3 years ago
0
Add README for PG_GencodeDB
#120
cgpu
closed
3 years ago
0
Review TransDecoder
#119
cgpu
closed
3 years ago
0
Updates ccs bam in run command for LR_IsoSeq3
#118
cgpu
closed
3 years ago
0
Add conf/test.config with ZENODO links to data
#117
cgpu
closed
3 years ago
2
Nextflow pipeline text in the paper
#116
gsheynkman
closed
3 years ago
0
Rmmiller rescue and resolve
#115
rmmiller22
closed
3 years ago
0
Download reference genome
#114
gsheynkman
closed
3 years ago
1
Rmmiller rescue and resolve
#113
rmmiller22
closed
3 years ago
0
Update local branch for merge
#112
rmmiller22
closed
3 years ago
0
Added files to Zenodo
#111
gsheynkman
closed
3 years ago
0
NMD ORF not called - adjust parameters for ORF calling?
#110
gsheynkman
closed
3 years ago
0
updated code to have main. added nextflow to pg_gencodedb and pg_make…
#109
bj8th
closed
3 years ago
0
orf calling nextflowified - TransDecoder separated
#108
bj8th
closed
3 years ago
0
nextflow added to 6 frame
#107
bj8th
closed
3 years ago
0
Removed DatabaseAnnoation. It is redundant with AccessionMapping module.
#106
gsheynkman
closed
3 years ago
0
Another PR to Main - add additional modules
#105
gsheynkman
closed
3 years ago
0
Add modules gencode db etc
#104
gsheynkman
closed
3 years ago
0
Dev
#103
bj8th
closed
3 years ago
0
Bj8th readme
#102
bj8th
closed
3 years ago
0
Write out distinct entires for same-pb-protein sequence but different gene
#101
gsheynkman
closed
3 years ago
0
Add nextflow io
#100
bj8th
closed
3 years ago
0
Clean up peptideanalysismodule
#99
gsheynkman
closed
3 years ago
1
Commands for Iso-Seq, SQANTI, CPAT for adding to nextflow
#98
gsheynkman
closed
3 years ago
1
Iso-Seq command code
#97
gsheynkman
closed
3 years ago
0
Add author name and ORCID to README.md
#96
gsheynkman
closed
3 years ago
0
Dev gloria
#95
gsheynkman
closed
3 years ago
0
Command run for MM
#94
gsheynkman
closed
3 years ago
1
Get CPAT Commands
#93
gsheynkman
closed
3 years ago
1
SQANTI command code
#92
gsheynkman
closed
3 years ago
1
testing - continuous testing?
#91
adeslatt
closed
3 years ago
0
Orf calling bug fix
#90
gsheynkman
closed
3 years ago
0
Add information to refine database metatable
#89
gsheynkman
closed
3 years ago
0
Adds nextflow referencetable, notes to SQANTI module.
#88
gsheynkman
closed
3 years ago
1
PG_ReferenceTables and the LR_TranscriptomSummary
#87
adeslatt
closed
3 years ago
0
Migrate dockerhub images to Quay
#86
adeslatt
closed
3 years ago
3
Dev rmmiller protein inference
#85
rmmiller22
closed
3 years ago
0
Dev rmmiller protein inference (#83)
#84
rmmiller22
closed
3 years ago
0
Dev rmmiller protein inference
#83
rmmiller22
closed
3 years ago
0
Add PULL_REQUEST.md template in .github/
#82
cgpu
closed
3 years ago
0
Update the help message parameters description refined_db_generation.nf
#81
cgpu
closed
3 years ago
0
Adds nextflow refined db
#80
cgpu
closed
3 years ago
0
Adds modules nextflow pseudocode
#79
cgpu
closed
3 years ago
0
Simi and Gloria - Update referencetable, transcriptome, and peptide modules
#78
gsheynkman
closed
3 years ago
0
Updated Transcriptomic Script
#77
gsheynkman
closed
3 years ago
0
Merging nextflow-code-containing branches into dev
#76
gsheynkman
closed
3 years ago
1
Removed unnecessary files from Transcriptome module
#75
kyuubi430
closed
3 years ago
0
Protein Inference
#74
bj8th
closed
3 years ago
1
Updates ORF calling Nextflow files
#73
cgpu
closed
3 years ago
0
Adds Dockerfile, environment.yml for SQANTI3
#72
cgpu
closed
3 years ago
0
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