Arcadia-Science peptigate issues

Arcadia-Science / peptigate

Peptigate ("peptide" + "investigate") predicts bioactive peptides from transcriptome assemblies or sets of proteins.

MIT License

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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