Prepare for the next Bioc release

What's Changed

• Enhance entrez_over_to_gsea function by adding msigdbr version check,… by @stemangiola in #322
• fix gene enrichment internal arguments by @stemangiola in #323
• take care of matrix conversion by @stemangiola in #321
• Resolve confounders without altering original columns by @stemangiola in #324
• fix docs by @stemangiola in #325

Full Changelog: v1.17.9...v1.19.1

Feb 2025

What's Changed

• if SummarizedExperiment is empty, do not fail by @stemangiola in #291
• fixes by @stemangiola in #293
• add method glmmTMB by @stemangiola in #296
• use Matrix library for sparse counts by @stemangiola in #294
• drop sample argument by @stemangiola in #300
• Fix bug reduce dimension by @stemangiola in #299
• De no forking by @stemangiola in #303
• Improve random effect dispersion by @stemangiola in #305
• Improve glmmseq by @stemangiola in #306
• Fix bioc error by @stemangiola in #310
• Fix interactions for de by @stemangiola in #311
• replace everywhere one_of by @stemangiola in #312
• Quantile normalise custom target by @stemangiola in #313
• return tibble with get action by @stemangiola in #314
• add method by @stemangiola in #307
• use matrix multiplication by @stemangiola in #315
• use a function to drop env by @stemangiola in #319
• Update confounders and filtering by @stemangiola in #318

Full Changelog: v1.11.7...v1.17.9

v1.11.7

What's Changed

• drop dataset by @stemangiola in #289
• Custom dispersion de by @stemangiola in #288
• Add fast quantile normalisation based on target sample, for 1000+ sample dataset. Add preprocess core method by @stemangiola in #290

Full Changelog: v1.11.6...v1.11.7

v1.11.6

What's Changed

• Add combat seq by @stemangiola in #281
• modify test to allow tidy mutate by @stemangiola in #284
• Dev by @stemangiola in #283

Full Changelog: v1.11.5...v1.11.6

v1.11.5 - random effect differential abundance and more

What's Changed

• Drop bind generics by @stemangiola in #271
• Allow custom assay for se de by @stemangiola in #274
• add tibble-based method by @stemangiola in #276
• added quantile normalisation by @stemangiola in #277
• Solve lme4 memory issue by @stemangiola in #278
• Identify abundant robustify by @stemangiola in #279
• Dev by @stemangiola in #275

Full Changelog: v1.11.3...v1.11.5

Release update for RMedicine2023

What's Changed

• Update introduction.Rmd by @stemangiola in #267
• Add LFC threshold tests for DESeq2 by @mikelove in #268

New Contributors

• @mikelove made their first contribution in #268

Full Changelog: v1.11.1...v1.11.3

DEVELOPMENT_3_17

What's Changed

• fixes by @stemangiola in #250
• Fix image2 by @mblue9 in #254
• change message frequency by @stemangiola in #255
• Dev by @stemangiola in #252
• Stemangiola patch 1 by @stemangiola in #257
• Release 3 15 by @stemangiola in #256
• Improve deconv docs by @stemangiola in #258
• Update check-bioc.yml by @mblue9 in #260
• add messaging by @stemangiola in #262

Full Changelog: v1.9.2...v1.11.1

Release for BioC2022

Changes in version 1.9.2, Bioconductor 3.16 Dev

• Improve aggregate_duplicates for tibble and SummarizedExperiment
• Fix epic deconvolution when using DelayedMatrix
• Allow as_SummarizedExperiment with multiple columns identifiers for .sample and .feature

What's Changed

• error if there are NAs in the .transcript column by @stemangiola in #248
• convert DelayedMatrix and fixed sample column name by @stemangiola in #247
• as_SE with multiple columns as input by @stemangiola in #249
• improve docs for deconvolution by @stemangiola in #246

Full Changelog: v1.7.4...v1.9.2

Dev Bioconductor 3.16

What's Changed

• Sparse counts by @stemangiola in #211
• Cibersort check 0 counts by @stemangiola in #217
• Update NEWS.rd by @mblue9 in #220
• Fix typo in DESeq raw result variable return by @antass in #223
• print message if reference is not defined by the user by @stemangiola in #226
• Cibersort check 0 counts by @stemangiola in #218
• Sparse counts by @stemangiola in #207
• Dev by @stemangiola in #227
• try fix by @stemangiola in #228
• Update actions to Bioc 3.14 by @mblue9 in #229
• For jian by @stemangiola in #230
• Dev by @stemangiola in #231
• add argument for scaling if not scaled by @stemangiola in #232
• Dev by @stemangiola in #233
• Update github action to Bioc 3.15 by @mblue9 in #234
• implement new vocabulary by @stemangiola in #237
• deprecate .contrasts and update tests by @stemangiola in #239
• avoid human annotation by @stemangiola in #238
• allow other feature column for SE by @stemangiola in #236
• Polish aggregation tibble by @stemangiola in #235
• implementation parallel cibersort by @stemangiola in #244
• deprecation untested by @stemangiola in #241
• Dev by @stemangiola in #242

New Contributors

• @antass made their first contribution in #223

Full Changelog: v1.5.5...v1.7.4

Bioconductor 3.14 - Used for BiocAsia2021

Merge pull request #216 from stemangiola/dev

Dev