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25 Open 102 Closed
25 Open 102 Closed
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Issues list

Error in rule setup_transfer_mods Bug Question
#240 opened Apr 3, 2024 by trom2
7
Enable running Spritz with singularity Compatibility New Feature
#239 opened Sep 13, 2023 by acesnik
Error in rule make_gene_quant_dataframe_ref Question
#237 opened Sep 1, 2023 by animesh
14
Update uniprot URLs to rest.uniprot from legacy.uniprot Maintenance
#226 opened Sep 6, 2022 by acesnik
Using Arabidopsis sequences for tests instead of yeast Maintenance
#224 opened Feb 19, 2022 by acesnik
1
FragPipe-ready fasta headers and redundancy reduction Compatibility
#221 opened Aug 24, 2021 by MiguelCos
5
Slight discrepancy in number of targets and decoys in withdecoys.fasta after mzLib decoy generation Improve Feature
#220 opened Aug 17, 2021 by acesnik
Option to generate separate databases for each input New Feature
#216 opened Jul 30, 2021 by acesnik
Docker vs Nextflow Question
#202 opened Feb 1, 2021 by DrDee79
4
Allow RefSeq references to be used New Feature
#194 opened Oct 9, 2020 by acesnik
Implement reference-free proteome generation New Feature
#193 opened Oct 9, 2020 by acesnik
Use other delimiter for combining accessions, etc Compatibility
#192 opened Sep 11, 2020 by acesnik
Implement variant finding for species without reference VCF New Feature
#186 opened Aug 25, 2020 by acesnik
Generating proteogenomic database for Pseudomonas with VCF called from WGS (or exome seq) data Question
#185 opened Aug 23, 2020 by animesh
6
Update genomes.csv for Ensembl versions 98 and 99 Maintenance
#171 opened May 29, 2020 by acesnik
Should we check for different codon tables in SnpEff when choosing a nonhuman species? Improve Feature
#164 opened Nov 16, 2019 by acesnik
Implement Mutect2 in the variant calling pipeline for calling somatic and germline mutations New Feature
#145 opened Nov 13, 2018 by acesnik New projects
2
Warn user that "MatePair" must be specified before running sample GUI Improve Feature
#131 opened Sep 20, 2018 by acesnik
Aligning long reads with STAR (e.g. nanopore) New Feature
#88 opened May 7, 2018 by acesnik New projects
2
Determine HLA genotype(s) New Feature Question
#73 opened Apr 25, 2018 by trishorts
1
Can we find back-spliced translation products? Question
#57 opened Mar 2, 2018 by acesnik
PLIER integration? Question
#52 opened Feb 6, 2018 by trishorts New projects
1
Allow UCSC references to be used New Feature
#31 opened Jan 18, 2018 by acesnik
Implement a transfer FDR calculation for TopHat novel splice junction peptides, since they're low #identifications Results Analysis
#10 opened Oct 24, 2017 by acesnik
1
Can we figure out the unknown start/stop codons for putative transcripts from proteomics data? Question
#5 opened Oct 24, 2017 by acesnik
2
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