v0.6.1

v0.6.1

• Fix --gene-level option
• Switch to job-pool package for multiprocessing
• Use specific libxml2 version to fix GUI build (#12)

v0.6.0

• Added support for FragPipe and Sage for LFQ data
• Support input files with byte order mark (#9)
• Added tool for entrapment FDR calculation and plotting
• Gui build fix (#8)
• Major code refactoring (camelCase to snake_case, new classes, better submodules)

v0.5.0

v0.5.0

• Added support for proteases that cleave before an amino acid, e.g. Asp-N, Lys-N
• Fix for empty score field in evidence file
• Add better detection of maxquant evidence files (#7)
• Added support for combining evidence files with different proteases
• Updated GUI to support different digestion parameters per evidence file
• Fix log levels in GUI
• Added example scripts and notebook for book chapter analysis
• Add check for shared peptides to protein groups that were filtered out because they had no reliable peptides
• Change peptide count to use score cutoff for peptide FDR instead of protein FDR
• Improved log messages

v0.4.0

v0.4.0

• Removed proteins without any PSMs below the FDR threshold from protein groups output. Setting the new --keep_all_proteins flag reverts to the old behavior.
• Added support for supplying multiple evidence files
• Added support for mokapot format and allow users to specify methods with custom toml files
• Add --fasta_contains_decoys flag and functionality
• Update llvmlite (#4)

v0.3.5

v0.3.5

• Added rescoring input (e.g. Prosit results) to GUI

v0.3.4

v0.3.4

• Added percolator input to GUI

v0.3.3

v0.3.3

• Add option for multiple evidence files and selecting digestion parameters in GUI

v0.3.2

v0.3.2

• Fix mokapot decoy filename
• Propagate argparse errors from pipeline scripts to logger

v0.3.1

v0.3.1

• Fixed missing methods folder in GUI

v0.3.0

v0.3.0

• Added make rules to reproduce manuscript figures
• Moved methods to toml files
• Update picking strategy to use leading proteins
• Add max_workers option for mokapot
• Add support for multiple threads in LFQ computation
• Fix non-functioning train_fdr option for mokapot