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Arcadia-Science
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peptigate
Peptigate ("peptide" + "investigate") predicts bioactive peptides from transcriptome assemblies or sets of proteins.
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update plmutils installation now that its public
#56
taylorreiter
closed
1 month ago
0
Should we filter out deeppeptide predicted propeptides?
#55
taylorreiter
opened
1 month ago
1
Deal with false mismatches in translation around Ns/Xs in nucleotide and amino acid sequences
#54
taylorreiter
closed
2 months ago
0
Orfipy outputs ORFs that contain the amino acid X, which breaks nucleotide conversion
#53
taylorreiter
closed
1 month ago
4
Update to newest plmutils (including new model) and fix other random small enhancements
#52
taylorreiter
closed
3 months ago
0
quick PR to update plmutils version
#51
taylorreiter
closed
3 months ago
0
Weird sORF results when changing the order of the input contigs file
#50
taylorreiter
closed
3 months ago
1
Change filtering for deepsig results
#49
taylorreiter
closed
3 months ago
0
report plmutils and deeppeptide scores in the predictions/peptide_predictions.tsv output file
#48
taylorreiter
opened
3 months ago
1
Change the input files to only take one transcriptome assembly file instead of two
#47
taylorreiter
closed
3 months ago
0
Quick PR to fix typos in README
#46
taylorreiter
closed
3 months ago
0
Add an evaluation script for plm-utils
#45
taylorreiter
closed
3 months ago
0
Cleanup unused envs, scripts, and file pointers
#44
taylorreiter
closed
3 months ago
0
Quick pr to add download code for autopeptideml models
#43
taylorreiter
closed
3 months ago
0
Consider requiring one file as input for the transcriptome assembly instead of splitting between short and long transcripts
#42
taylorreiter
closed
3 months ago
0
Documentation PR!
#41
taylorreiter
closed
3 months ago
0
Refactor to reduce duplication when there is only protein as input
#40
taylorreiter
closed
4 months ago
1
make changes so protein only input files can be used
#39
taylorreiter
closed
4 months ago
1
Consider including bioactivity prediction with PeptideRanker or similar, or recommending it as a follow up step in documentation
#38
taylorreiter
opened
5 months ago
0
Consider reframing response to `if not utils.verify_translation(...)`
#37
taylorreiter
opened
5 months ago
0
Consider moving the function `extract_ripp_sequences()` in `run_nlpprecursor.py` to a new script `extract_nlpprecursor_sequences.py`
#36
taylorreiter
opened
5 months ago
0
In scripts/extract_plmutils_nucleotide_sequences.py `extract_positions_and_frame()`, consider switching to regex
#35
taylorreiter
opened
5 months ago
0
Consider adding PepScore to filter peptide predictions to stable peptides
#34
taylorreiter
opened
5 months ago
0
Consider adding DeepLoc or other tool to predict subcellular localization of predicted peptides
#33
taylorreiter
opened
5 months ago
0
Generate a manifest of the peptigate run
#32
taylorreiter
opened
5 months ago
0
Output nucleotide sequences for peptide predictions
#31
taylorreiter
closed
5 months ago
0
Consider refactoring `extract_deeppeptide_sequences.py`, `extract_plmutils_nucleotide_sequences.py`, & `scripts/run_nlpprecursor.py`
#30
taylorreiter
opened
5 months ago
0
Consider automated testing framework
#29
taylorreiter
opened
5 months ago
0
consider separating final results out into their own directory
#28
taylorreiter
closed
4 months ago
0
Parameterize the database used for checking if sequences are from fragment transcripts that encode long protein coding genes
#27
taylorreiter
opened
5 months ago
0
Filter input transcripts by hits to uniref50 before applying plmutils for sORF identification
#26
taylorreiter
closed
5 months ago
4
considering moving blast built databases from outputs to inputs dir
#25
taylorreiter
opened
5 months ago
2
Consider filtering plmutils peptide predictions by removing those that have hits to long (>100aa) proteins in swissprot, NR, or other large BLAST databases
#24
taylorreiter
closed
5 months ago
4
Bug fixes from first run
#23
taylorreiter
closed
5 months ago
0
Add in sORF prediction to peptigate using plmutils
#22
taylorreiter
closed
6 months ago
2
consider outputting nucleotide sequences that underly the peptides
#21
taylorreiter
closed
4 months ago
0
update snakefile to train model for plmutils instead of rnasamba
#20
taylorreiter
closed
6 months ago
0
record instance size for running peptigate
#19
taylorreiter
closed
4 months ago
0
Remove NRPS search rules & files
#18
taylorreiter
closed
6 months ago
1
Remove NRPS modules in favor of using antismash for annotation
#17
taylorreiter
closed
6 months ago
0
Consider outputting two TSV files instead of one from combine_peptide_annotations.R
#16
taylorreiter
closed
5 months ago
1
update autopeptideml modeldir input string
#15
taylorreiter
closed
3 months ago
0
Autopeptideml efficiency
#14
taylorreiter
opened
6 months ago
2
Consider including conopeptide prediction in the pipeline
#13
taylorreiter
closed
6 months ago
3
Add rule to combine peptide annotation outputs
#12
taylorreiter
closed
6 months ago
0
Brainstorming how to filter down to cleavage peptides that are potentially real
#11
taylorreiter
closed
5 months ago
6
Add rule to classify peptide bioactivity with the autopeptideml tool
#10
taylorreiter
closed
6 months ago
1
Consider changing snakemake input and output variable rules
#9
taylorreiter
closed
4 months ago
2
Change output peptide fasta ID for predicted peptide FASTA files to contain info in header instead
#8
taylorreiter
opened
6 months ago
4
Add rules to characterize peptide sequences
#7
taylorreiter
closed
6 months ago
0
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