NEWS
scifer 1.15.1
BUG FIXES
- Fix
igblast() crashing with the cryptic error "argument of length 0" when
the igblast output contained no AIRR header line. The wrapper now returns
NULL gracefully and reports the captured igblast/conda output so build-time
failures are diagnosable. This fixes the failing test-igblast.R check on
the Bioconductor build machines.
- Make the "returns a data.frame object" test skip (instead of erroring) when
the igblast/conda environment is unavailable in the test environment.
- Guard a division-by-zero in
igblastwrap.py when zero sequences are
processed.
scifer 1.12.1
- fix minor bug that crashed
quality_report when some sequences had problematic quality and had NA or Inf values
- this affects
summarise_quality and summarise_abi_file
scifer 1.9.1
- fix igblast cdr3 bug with the contribution of Sebastian Ols (@sebbeols)
- this affects igblast.R function, but mainly the igblast wrapper igblastwrap.py
scifer 1.8.1
- Update citation, scifer is now published in ImmunoInformatics (DOI: 10.1016/j.immuno.2024.100046).
scifer 1.8.0
NEW FEATURES
- New igblast wrapper function to run igblast on fasta sequences
- igblast function returns the output from a local igblast run with any custom database
- New function requires additional steps for ARM processors, please read the README
scifer 1.7.1 (2024-04-24)
BUG FIXES
- Fix compensation bug due to different compensation matrix positions in different
.fcs file versions
- update minor nomenclature to AIRR-standards, column
file_ID to sequence_id
- Fix error of
HC_individualized_report.Rmd file not being found
NEW FEATURES
- Update quality thresholds based on a large B cell receptor test dataset
scifer 0.99.4 (2022-10-31)
- Version bump to bioconductor, updated description
scifer 0.99.3 (2022-09-20)
BUG FIXES
- Fix NOTE when building on windows computer
scifer 0.99.2 (2022-09-08)
NEW FEATURES
- Update vignette according to Bioconductor
- Added unit tests for functions
SIGNIFICANT USER-VISIBLE CHANGES
- Split function fcs_processing() into two functions:
- fcs_processing()
- fcs_plot()
BUG FIXES
- Minor changes to avoid possible bugs
scifer 0.99.1 (2022-08-26)
- Version bump to fix Bioconductor building error
scifer 0.99.0 (2022-08-10)
- Adapting package for Bioconductor submission
scifer 0.98.0 (2022-08-09)
- Major changes in functions
- nomenclature and all documentation were added following R style guidelines
- Processing flow cytometry data and adding to the quality_report() function
scifer 0.1.0 (2022-04-15)
scifer 0.0.1 (2020-08-10)
- Primordial package created with simple functions and bugs