Tidybulk Versions Save

What's Changed

• drop dataset by @stemangiola in https://github.com/stemangiola/tidybulk/pull/289
• Custom dispersion de by @stemangiola in https://github.com/stemangiola/tidybulk/pull/288
• Add fast quantile normalisation based on target sample, for 1000+ sample dataset. Add preprocess core method by @stemangiola in https://github.com/stemangiola/tidybulk/pull/290

Full Changelog: https://github.com/stemangiola/tidybulk/compare/v1.11.6...v1.11.7

What's Changed

• Add combat seq by @stemangiola in https://github.com/stemangiola/tidybulk/pull/281
• modify test to allow tidy mutate by @stemangiola in https://github.com/stemangiola/tidybulk/pull/284
• Dev by @stemangiola in https://github.com/stemangiola/tidybulk/pull/283

Full Changelog: https://github.com/stemangiola/tidybulk/compare/v1.11.5...v1.11.6

What's Changed

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

Full Changelog: https://github.com/stemangiola/tidybulk/compare/v1.11.3...v1.11.5

What's Changed

• Update introduction.Rmd by @stemangiola in https://github.com/stemangiola/tidybulk/pull/267
• Add LFC threshold tests for DESeq2 by @mikelove in https://github.com/stemangiola/tidybulk/pull/268

New Contributors

• @mikelove made their first contribution in https://github.com/stemangiola/tidybulk/pull/268

Full Changelog: https://github.com/stemangiola/tidybulk/compare/v1.11.1...v1.11.3

What's Changed

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

Full Changelog: https://github.com/stemangiola/tidybulk/compare/v1.9.2...v1.11.1

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 https://github.com/stemangiola/tidybulk/pull/248
• convert DelayedMatrix and fixed sample column name by @stemangiola in https://github.com/stemangiola/tidybulk/pull/247
• as_SE with multiple columns as input by @stemangiola in https://github.com/stemangiola/tidybulk/pull/249
• improve docs for deconvolution by @stemangiola in https://github.com/stemangiola/tidybulk/pull/246

Full Changelog: https://github.com/stemangiola/tidybulk/compare/v1.7.4...v1.9.2

What's Changed

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

New Contributors

• @antass made their first contribution in https://github.com/stemangiola/tidybulk/pull/223

Full Changelog: https://github.com/stemangiola/tidybulk/compare/v1.5.5...v1.7.4

This is the version was used to build the Genome Biology article "tidybulk: an R tidy framework for modular transcriptomic data analysis"