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Releases: Nesvilab/philosopher

Philosopher 5.1.0

19 Dec 20:47
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Added

  • Supported IBT-16 isobaric tag
  • Extended support for up to 32 isobaric labels.
  • Added the 'minPepLen' control option for protein probability assignment
  • Added the dbbin option to resue the prebuilt db.bin file

Changed

  • Used unique+razor peptides only for PSM-protein level roll up
  • For plex with 0 PSMs, let philosopher print a warning and exit normally
  • Excluded decoys from protein quantification (protein.tsv)
  • Removed the warning message for running 'workspace --clean' in a clean direcotry

Fixed

  • Fixed a problem occurring when parsing custom database with headers starting with '>AT'
  • Fixed a bug related to summed intensites in protein.tsv
  • Fixed a bug causing empty intensities in msstats.tsv related with multiplex TMT11 data.
  • Fixed a crash when there are non-zero TMT intensities and removelow > 0
  • Updated the purity calculation

Philosopher 5.0.0

31 May 21:19
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Added

  • Added the protein start and end positions to ions and peptides report.
  • ProtXML reading parallelization.
  • Added a new Extended Peptide column to the PSM report containing the flanking regions of peptides.
  • Group-based FDR scoring option (based on the group labeled passed by MSFragger).
  • Support for sCLIP isobaric tags.

Changed

  • Rolled back the FASTA header checking for IonQuant.
  • Improved the FASTA header detection and parsing.
  • PTMProphet was updated to v6.2.0.
  • Faster processing speed and reduced memory usage due to major improvements in IO operations and database reading (@guoci).
  • The purity column will always be visible in the PSM table.
  • Updated the MSstats report for TMT data, making them compatible with MSstats and MSstats-PTM.

Fixed

  • Updated razor mapping rules to reinforce classifying decoy razor proteins.
  • Fixed a problem where protein names and genes would not be tagged with the decoy tag.

Philosopher 4.8.1

20 Jan 17:43
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Added

  • FASTA header verification for IonQuant

Changed

  • New version annoucements will happpen for all updates, including minor changes

Fixed

  • Fixed an issue that would not udpate PSMs with razor IDs and description

Docker

  • docker pull prvst/philosopher:4.8.1
  • docker pull prvst/philosopher:latest

Philosopher 4.8.0

11 Jan 19:54
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Fixed

  • Fixed the protein coverage calculations with partially overlapping and subsumed peptides
  • Fixed an issue where peptides would map to multiple locations in the protein after having I/L converted (Needs to be used with MSFragger v3.6.1 or higher)
  • Fixed an issue with report tables having no isobaric labels being reported

Philosopher 4.7.0

23 Dec 16:53
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Added

  • Adjusted the peptide-to-protein mapping due to I/L replacement rules
  • Adjusted the protein FDR calculation rules.

Changed

  • Removed the normalization done at the protein level in label quant
  • Improved the protein filter for small scale analyses

Fixed

  • Adjusted the msstats file format, added purity to all plex sizes
  • Fixed the protein coverage calculations
  • Fixed repeated isobaric values that would eventually show up in the protein table

Philosopher 4.6.0

02 Dec 21:33
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Added

  • Added new flag --removecontam to the report command to remove contaminants from the reports
  • Added a new combined_psm report to abacus (beta)

Changed

  • Updated the TMT-Integrator to match with the version v4.0.0
  • Updated the pickedFDR filter
  • The pipeline command now accepts annotation files with prefixes
  • Updated PTMProphet to the latest release
  • Updated the database fetch with the new UniProt API (The new API is still unstable, people might experience hiccups with certain cases, especially non-model organisms without reviewed sequences)

Fixed

  • Contaminant tags are now added to Human sequences as well
  • Added a fix for errors causes by division-by-zero errors (PR by @chhh)
  • Fixed the protein coverage calculations to consider all peptides
  • Several minor fixes and updates

Philosopher 4.4.0

05 Jul 17:37
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Fixed

  • Issue with the database command only fetching the human FASTA.

Docker

  • docker pull prvst/philosopher:4.4.0
  • docker pull prvst/philosopher:latest

Philosopher 4.3.0

29 Jun 20:08
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Fixed

  • Updated the Endpoint from UniProt, fixing the database fetching issue.

Docker

  • docker pull prvst/philosopher:4.3.0
  • docker pull prvst/philosopher:latest

Philosopher 4.2.2

27 May 15:04
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Added

  • Decoys tag now appear inthe Gene and ProteinID
  • Support for TAIR database
  • Support for neXtProt database
  • Support for MSBooster scores which now appear in the PSM table

Fixed

  • Minor bugs andd issues were fixed

Docker

  • docker pull prvst/philosopher:4.2.2
  • docker pull prvst/philosopher:latest

Philosopher 4.2.1

05 Apr 21:52
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Added

  • Added support for TMT 18
  • Added option for contaminant tags in the database.

Changed

  • Added the parsing rules from the Prophets to the protein description.
  • Removed RawReader.
  • Improved processing speed and resource usage.
  • Reduced binary size.

Fixed

  • Several bugs and code fixes added.
  • Fixed issue with TMT 6 plex quantification.

Docker

  • docker pull prvst/philosopher:4.2.1
  • docker pull prvst/philosopher:latest