NEWS
immGLIPH 0.99.5
- Vignette: removed undefined variable references (
mouse_tcr_data,
contig_list placeholder, ... in custom_ref). Five previously
unevaluated chunks now run during build, using tempdir(),
scRepertoire::contig_list, the bundled gliph_sce, and a real
reference data frame built from gliph_input_data. The three
remaining eval = FALSE chunks are limited to BiocManager::install()
calls and the optional getGLIPHreference() network download.
- Consolidated duplicated column-type coercion
for loops in
loadGLIPH(), plotNetwork() and clusterScoring() into a single
lapply()-based helper, .coerce_numeric_cols().
immGLIPH 0.99.4
- Added a Validation section to the README with concordance metrics
against the published GLIPH and GLIPH2 cluster vectors from
Glanville et al. (2017) and Huang et al. (2020). With paper-matched
parameters, immGLIPH reproduces the published cluster vectors at
ARI 0.985 (Glanville) and 0.863 (Huang) on the intersection of
shared CDR3s. Full benchmark code lives at
BorchLab/immGLIPH-benchmark.
- Fixed
clusterScoring() failure in the clonal-expansion-enrichment
test when a cluster contains more members than the reference pool
has rows. The null draw now uses replace = TRUE (bootstrap),
matching the V-gene null and the statistically appropriate choice
for resampling. Surfaced on the Huang 2020 benchmark.
immGLIPH 0.99.3
- Replaced
foreach/doParallel with BiocParallel for parallelization
across all functions per Bioconductor recommendations.
- Replaced
devtools::install_github() references with
BiocManager::install() in vignette and error messages.
- Updated vignette to use
SingleCellExperiment instead of Seurat for
the single-cell workflow example.
- Fixed
combineTCR() example in vignette (removed obsolete cells
argument).
- Made more vignette code chunks evaluable (
clusterScoring(),
deNovoTCRs(), plotNetwork() examples).
- Noted that
scRepertoire and immApex are Bioconductor packages.
- Replaced iterative for-loop list growing with vectorized alternatives
(
lapply(), vapply(), Reduce()).
- Standardized code spacing around operators and after commas per
Bioconductor coding style.
immGLIPH 0.99.2
- Fixing roxygen documentation issue creating warnings.
immGLIPH 0.99.1
- Moved reference repertoire data hosting from GitHub releases to Zenodo
(https://zenodo.org/records/18925758) per Bioconductor requirements.
- Updated
getGLIPHreference() to download from Zenodo.
immGLIPH 0.99.0
- Initial Bioconductor submission
- R implementation of GLIPH and GLIPH2 algorithms for TCR clustering
- Integration with scRepertoire ecosystem via immApex
- Interactive network visualization with plotNetwork()
- De novo TCR sequence generation with deNovoTCRs()