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TBSignatureProfiler (development version)

Bug Fixes

Major Changes

Minor Changes

  • Updated the github and website introductions.
  • Added Natarajan_7, Kaul_3 signatures
  • Shortened some example run times

TBSignatureProfiler 1.8.0

Bug Fixes

  • Fixed gene in RESPONSE5 (PNN to RP11-295G20.2) in TBsignatures and TBcommon objects. (Stanley M. Kimbung)
  • Fixed a bug in the singscore algorithm called from runTBsigProfiler() that would not allow for the scoring of user-provided signatures.
  • Fixed the TB_hiv data to remove unnecessary factor level of Disease metadata.
  • Fixed the row numbers of existing sigAnnotData and common_sigAnnotData objects, and added code to update them after new signatures are added.

Major Changes

  • If any signatures in the object used with runTBsigProfiler() have <2 genes present in the given sample, the signatures will not be scored. This may affect existing scripts.

Minor Changes

  • Reorganized code for OriginalModel.R for clarity.
  • Added 4 new signatures (Tabone_OD_11/TB12, Tabone_RES_25/EarlyRESP-TB25, Tabone_RES_27/TREAT-TB27, Long_RES_10)
  • Updated the website interface
  • Changed HGNChelper installation to be checked during profiling if update_genes = TRUE
  • Reorganized code in mkAssay() for clarity. The output_name argument is now appended to all output assays, whereas previously it was only appended to the log of the input assay.

TBSignatureProfiler 1.6.0

Bug Fixes

  • Fixed some package tests for the profile.R, OriginalModel.R scripts to increase coverage

Major Changes

  • Added the gene_update parameter to runTBsigProfiler() to allow users to check signature/sample gene names for excel mogrified or outdated gene symbols
  • Updated gene symbols for original models functions
  • Added Chendi_HIV_2 signature (8/24)
  • Removed Mendelsoh_RISK_11 as it was originally published in Darboe_RISK_11. Changed Darboe_RISK_11 to RISK11 in common objects. (Thomas Scriba)

Minor Changes

  • Rewrote runTBsigProfiler() to be shorter and easier to maintain

TBSignatureProfiler 1.5.0

  • 68 signatures currently available

Bug Fixes

  • Fixed incorrect names of signatures in Tbcommon and common_sigAnnotData objects

Major Changes

  • Added Zimmer_RES_3, Gong_OD_4, Bloom_RES_268, and Bloom_RES_558
  • Added Sivakumaran_11 and Mendelsoh_RISK_11 signatures
  • Added Estevez_133, Estevez_259, LauxdaCosta_OD_3, and Maertzdorf_15 signatures to the package
  • Added Chen_HIV_4, Gliddon_HIV_3, Gliddon_2_OD_4, Kulkarni_HIV_2, and Heycken_FAIL_22 signatures
  • Added a COVIDsignatures object to the package that can be used to profile COVID-19 gene transcript signatures, thanks to collaborator Dylan Sheerin (WEHI)
  • Added functions to evaluate some signatures using their original models from Johnson lab member Xutao Wang

Minor Changes

  • Added mention of COVIDsignatures object to main vignette and website
  • Included the OG models tutorial on website (Xutao Wang)
  • Added addTBsignature() to more easily facilitate updating signatures in package
  • Added pROC option to obtain confidence intervals on AUC values as part of
  • Added citation for newly published paper