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TBSignatureProfiler (development version)
- Updated the github and website introductions.
- Added Natarajan_7, Kaul_3 signatures
- Shortened some example run times
- 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.
- 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.
- 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.
- Fixed some package tests for the profile.R, OriginalModel.R scripts to increase coverage
- 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gene_update parameter to runTBsigProfiler() to allow users to check signature/sample gene names for excel mogrified or outdated gene symbols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)
- Rewrote runTBsigProfiler() to be shorter and easier to maintain
- 68 signatures currently available
- Fixed incorrect names of signatures in
- 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
- Added mention of COVIDsignatures object to main vignette and website
- Included the OG models tutorial on website (Xutao Wang)
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